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0.05634877 + 18 -8.85295084 -5.43068897 -6.07158450 -0.01116612 -0.15659120 0.06801420 0.17108891 + 18 -2.06020760 -5.36948190 5.13702553 0.00414250 0.03576489 -0.04696898 0.05918084 + 18 0.83742622 -4.64635091 -1.75618386 -0.00568923 0.00855457 0.06046984 0.06133637 + 18 -7.99106543 0.18786198 2.20800008 -0.06737724 -0.01030777 -0.07996295 0.10507148 + 18 -2.09661325 -4.82996618 1.16820195 0.01783501 -0.03411389 -0.04807805 0.06159013 + 18 -9.01828044 2.94401169 -4.77887529 0.02628327 0.03220709 0.02520879 0.04861677 + 18 4.48714574 2.41592657 0.36561988 -0.03683451 0.02570320 -0.02585049 0.05182358 + 18 -4.70892494 4.07503221 1.40252271 0.02893342 -0.01112960 0.02487799 0.03974827 + 18 -3.05937341 1.40499744 -6.78149762 0.04385072 -0.01287660 -0.03242614 0.05603702 + 18 -1.12432249 8.28407964 5.48964100 -0.00637160 -0.03155624 0.01508465 0.03555194 + 18 -0.15581830 -4.32018855 9.35533971 0.02611029 -0.04129996 0.10891882 0.11937647 + 18 -5.22167731 -2.91561915 5.35616981 0.05874345 -0.04888318 -0.02017128 0.07903948 + 18 8.33859224 4.39826089 7.11780713 -0.04451774 0.07063194 -0.00058151 0.08349274 + 18 8.89737450 3.81748405 -8.12035728 -0.00481737 -0.00415698 -0.00259410 0.00687146 + 18 -5.71289391 3.73756466 -6.47490368 -0.01793246 0.06909206 0.05971087 0.09306274 + 18 -9.08140970 -2.60072846 -4.30657490 0.00250483 -0.00955777 0.16746164 0.16775287 + 18 4.49562817 -0.55105181 2.12065081 -0.11331083 -0.02902065 0.04002209 0.12362569 diff --git a/EXAMPLES/Argon/HICOLM.in b/EXAMPLES/Argon/HICOLM.in new file mode 100644 index 0000000..1c0d782 --- /dev/null +++ b/EXAMPLES/Argon/HICOLM.in @@ -0,0 +1,213 @@ +# Method to be used: Molecular dynamics or Tight-binding + +&INIT +method MD +&END + +# Unitary cell coordinates + +&CELL + 30.0000000000 0.0000000000 0.0000000000 + 0.0000000000 30.0000000000 0.0000000000 + 0.0000000000 0.0000000000 30.0000000000 +&END + +# Atomic coordinates + +&COORD +reuse 0 +natom 166 + 18 14.866066 4.506193 0.011229 1 1 + 18 -0.026775 25.032044 -0.058474 1 1 + 18 -0.007374 -0.005671 15.068497 1 1 + 18 -0.018258 25.027887 5.441493 1 1 + 18 -0.033299 3.797870 5.240887 1 1 + 18 -0.072216 25.024965 21.692485 1 1 + 18 22.502908 8.257176 25.015072 1 1 + 18 7.416517 20.800058 21.804266 1 1 + 18 25.011774 -0.031238 25.027363 1 1 + 18 15.712724 19.301322 25.013964 1 1 + 18 -0.018036 -0.001323 0.688159 1 1 + 18 10.781784 25.028384 4.297809 1 1 + 18 15.886098 19.915393 5.174089 1 1 + 18 10.820075 13.396565 9.818430 1 1 + 18 -0.003927 5.454994 -0.003386 1 1 + 18 9.303483 15.428542 4.937981 1 1 + 18 6.463616 10.026969 25.009992 1 1 + 18 10.132973 4.197061 18.153771 1 1 + 18 25.007790 15.284642 12.898792 1 1 + 18 10.275546 8.975539 21.003423 1 1 + 18 19.708780 25.050877 25.084803 1 1 + 18 20.044912 -0.090577 22.666220 1 1 + 18 4.610358 8.448293 0.003026 1 1 + 18 22.260583 -0.096990 4.392585 1 1 + 18 17.765588 7.793605 9.811652 1 1 + 18 15.445958 25.005017 7.211765 1 1 + 18 0.002054 15.070483 13.427050 1 1 + 18 -0.014550 11.424538 0.024200 1 1 + 18 20.154288 1.601715 12.721034 1 1 + 18 2.500472 20.990380 2.684296 1 1 + 18 19.858737 15.506750 25.022277 1 1 + 18 9.830775 6.717437 -0.035726 1 1 + 18 10.872169 5.190000 6.115892 1 1 + 18 3.103384 8.305774 5.539542 1 1 + 18 24.995164 12.533906 -0.022092 1 1 + 18 20.447906 20.306518 22.402935 1 1 + 18 21.812525 25.063113 20.003399 1 1 + 18 15.274276 25.017649 12.876799 1 1 + 18 25.025561 11.935988 17.261725 1 1 + 18 -0.004349 10.115627 11.039982 1 1 + 18 13.701101 9.865179 6.739712 1 1 + 18 8.759290 10.514138 15.945606 1 1 + 18 25.029879 13.142006 25.033388 1 1 + 18 20.634012 25.038894 5.389036 1 1 + 18 7.974504 22.684052 15.332255 1 1 + 18 25.031512 -0.032925 9.142666 1 1 + 18 12.695801 20.047592 20.460502 1 1 + 18 15.202360 16.121191 11.721408 1 1 + 18 25.023821 20.735264 12.166353 1 1 + 18 12.769822 0.003610 9.503357 1 1 + 18 8.312003 10.067551 5.662563 1 1 + 18 14.803237 -0.011353 25.015318 1 1 + 18 19.626858 16.061527 3.992865 1 1 + 18 4.827270 4.368015 14.915853 1 1 + 18 -0.022816 15.435527 18.914779 1 1 + 18 -0.021728 6.576274 20.126306 1 1 + 18 2.996915 4.528211 24.429629 1 1 + 18 10.417709 18.758916 12.353412 1 1 + 18 7.982907 20.717249 2.341305 1 1 + 18 25.064244 1.541541 -0.045829 1 1 + 18 9.338984 -0.012861 5.205034 1 1 + 18 10.740296 20.284792 7.079865 1 1 + 18 5.474606 6.512770 19.938665 1 1 + 18 19.286952 6.984246 20.224438 1 1 + 18 19.669447 12.187039 18.484119 1 1 + 18 14.949016 3.692756 13.031407 1 1 + 18 5.438736 16.447774 -0.014188 1 1 + 18 14.496818 9.993269 -0.029267 1 1 + 18 -0.031539 19.201515 8.108894 1 1 + 18 3.925904 16.457278 5.452993 1 1 + 18 25.032414 20.736863 18.924609 1 1 + 18 8.719787 12.070965 0.556746 1 1 + 18 4.669933 4.281067 8.944706 1 1 + 18 10.649141 25.005102 9.901246 1 1 + 18 14.468056 14.227776 3.479657 1 1 + 18 5.788276 8.976296 11.580583 1 1 + 18 6.620633 -0.012526 17.716649 1 1 + 18 15.138882 3.406846 20.719578 1 1 + 18 4.978051 25.043178 19.295179 1 1 + 18 16.613188 25.006202 18.211173 1 1 + 18 -0.064920 12.750406 6.212845 1 1 + 18 11.282175 -0.006339 14.798213 1 1 + 18 -0.005372 14.543206 24.341924 1 1 + 18 23.155357 15.857982 20.633761 1 1 + 18 10.492184 17.570495 25.022739 1 1 + 18 19.625283 6.970079 1.400238 1 1 + 18 17.693511 20.810670 10.288353 1 1 + 18 4.055342 23.680370 25.068627 1 1 + 18 -0.020845 -0.001833 9.568371 1 1 + 18 5.472288 25.010447 -0.005628 1 1 + 18 4.764384 17.199854 25.006233 1 1 + 18 17.341620 25.019539 0.983551 1 1 + 18 16.307209 4.921347 5.318798 1 1 + 18 5.438384 -0.002081 -0.002181 1 1 + 18 14.421425 7.469990 17.082546 1 1 + 18 18.421465 4.571364 25.090042 1 1 + 18 11.208496 16.941000 -0.022219 1 1 + 18 16.949470 16.562434 20.407691 1 1 + 18 5.652760 19.800698 9.471153 1 1 + 18 25.000404 18.641807 25.001649 1 1 + 18 8.735469 17.676248 17.474753 1 1 + 18 19.916278 14.519426 9.393126 1 1 + 18 0.421620 25.011382 16.215142 1 1 + 18 5.542658 14.493446 10.910570 1 1 + 18 16.554706 18.232884 -0.018676 1 1 + 18 22.253423 19.191934 7.673343 1 1 + 18 4.662031 14.163166 16.329482 1 1 + 18 22.744866 25.027218 -0.042171 1 1 + 18 20.722513 25.016114 12.125764 1 1 + 18 -0.023070 -0.029852 25.021000 1 1 + 18 21.379700 4.431322 7.386669 1 1 + 18 2.366213 9.183655 15.914498 1 1 + 18 1.846504 1.404157 20.051325 1 1 + 18 17.617102 10.583364 24.031909 1 1 + 18 9.386389 25.030044 25.032716 1 1 + 18 16.742766 11.316021 13.909822 1 1 + 18 25.043842 -0.026163 14.642394 1 1 + 18 6.326105 -0.015297 11.952476 1 1 + 18 7.660696 14.096237 21.509095 1 1 + 18 19.674573 10.735442 5.408891 1 1 + 18 10.420183 -0.002991 21.693210 1 1 + 18 19.863582 16.127886 14.652423 1 1 + 18 25.027370 4.950298 11.469879 1 1 + 18 3.023804 20.414208 14.565541 1 1 + 18 -0.000804 4.764796 12.311733 1 1 + 18 12.541449 12.466778 25.001345 1 1 + 18 9.723939 4.276210 11.416525 1 1 + 18 24.988057 7.037018 0.159122 1 1 + 18 19.500728 12.287872 -0.006207 1 1 + 18 2.239617 20.327598 20.008663 1 1 + 18 18.033789 -0.012084 7.910268 1 1 + 18 23.276160 10.124956 12.106590 1 1 + 18 14.940778 20.163768 15.441240 1 1 + 18 5.291896 25.028284 11.142488 1 1 + 18 15.387153 -0.021632 3.089311 1 1 + 18 -0.025412 9.085301 25.020446 1 1 + 18 25.080896 16.656079 3.617531 1 1 + 18 25.011617 6.459029 16.758596 1 1 + 18 -0.033327 20.002644 25.006534 1 1 + 18 -0.040390 16.924255 -0.009865 1 1 + 18 25.072003 24.099776 24.327503 1 1 + 18 25.025271 25.005582 8.700197 1 1 + 18 10.902818 0.621313 -0.029339 1 1 + 18 21.911084 19.591087 0.010466 1 1 + 18 21.456798 2.448740 17.996724 1 1 + 18 3.859230 -0.063520 5.671158 1 1 + 18 8.454166 4.900019 25.003552 1 1 + 18 5.464798 24.652132 5.652739 1 1 + 18 2.959485 11.294379 20.964599 1 1 + 18 10.476421 25.011414 19.641880 1 1 + 18 -0.097034 23.975376 10.839009 1 1 + 18 6.019576 -0.031270 25.001305 1 1 + 18 25.012058 8.129786 5.549288 1 1 + 18 25.098541 22.141805 4.005183 1 1 + 18 13.514493 7.053664 25.010337 1 1 + 18 6.202977 4.331085 3.338997 1 1 + 18 19.565715 1.651056 -0.071398 1 1 + 18 25.011300 4.487799 21.892843 1 1 + 18 25.005729 13.130775 7.838202 1 1 + 18 25.030944 25.075151 15.543943 1 1 + 18 20.245545 21.383570 16.227860 1 1 + 18 19.891366 6.700870 14.765127 1 1 + 18 16.708101 -0.005913 16.702053 1 1 + 18 12.541111 13.580298 19.026428 1 1 + 18 14.558069 24.389809 23.275288 1 1 + 18 12.709898 22.231731 -0.027511 1 1 +&END + +# Molecular dynamics parameters + +&MD +nhist 1000 +preext 1000 +text 73 +ntrialmax 100000 +nrelax 1 +timestep 0.001 +ensemble npt 0.1 0.1 4.9d-5 +rcutoff 9.0 0.1 +&END + +# Force field parameters + +&FORCE +vdw 1 +1 1 lj 0.0103235 3.405 +&END + +# Molecules to be considered + +&MOLEC +molecs 1 +Ar 166 1 +&END diff --git a/EXAMPLES/H2O/HICOLM.in b/EXAMPLES/H2O/HICOLM.in new file mode 100644 index 0000000..7d43cc2 --- /dev/null +++ b/EXAMPLES/H2O/HICOLM.in @@ -0,0 +1,254 @@ +# Method to be used: Molecular dynamics or Tight-binding + +&INIT +method MD +&END + +# Unitary cell coordinates + +&CELL + 12.8511897900 0.0000000000 0.0000000000 + 0.0000000000 12.8511897900 0.0000000000 + 0.0000000000 0.0000000000 12.8511897900 +&END + +# Atomic coordinates + +&COORD +reuse 1 +natom 192 + 8 11.490614 4.977578 2.213542 1 1 + 1 10.617955 5.178310 2.673797 2 1 + 1 11.656752 5.609023 1.423832 3 1 + 8 3.568773 0.428749 1.676783 1 1 + 1 3.753054 0.671842 2.692942 2 1 + 1 4.235152 12.409057 1.465003 3 1 + 8 5.765885 4.424698 5.708926 1 1 + 1 6.230528 3.944603 4.993301 2 1 + 1 5.473490 5.323711 5.220988 3 1 + 8 6.622399 12.445354 4.797142 1 1 + 1 5.761508 0.206994 4.519395 2 1 + 1 7.321598 0.135309 4.208010 3 1 + 8 4.742895 6.950043 12.598664 1 1 + 1 4.891173 6.116444 0.448978 2 1 + 1 5.489101 7.582496 12.523657 3 1 + 8 11.319277 0.712339 8.161936 1 1 + 1 11.023127 1.700559 7.924778 2 1 + 1 12.161530 0.646368 7.627084 3 1 + 8 8.332083 1.069372 2.997345 1 1 + 1 7.922770 1.235015 1.970486 2 1 + 1 8.998524 0.371668 2.846163 3 1 + 8 0.554587 3.026336 11.162126 1 1 + 1 1.431699 3.437657 10.725039 2 1 + 1 0.930121 2.471483 11.957962 3 1 + 8 7.177908 1.317399 0.512644 1 1 + 1 7.602330 0.828303 12.366451 2 1 + 1 6.311053 1.817227 0.375476 3 1 + 8 3.133984 2.888945 6.931818 1 1 + 1 3.206707 1.924759 6.687747 2 1 + 1 3.811992 3.391418 6.346094 3 1 + 8 9.034720 5.764196 3.362020 1 1 + 1 8.389882 6.540173 2.992220 2 1 + 1 9.238424 6.011376 4.348626 3 1 + 8 5.182476 6.242541 3.928063 1 1 + 1 4.883635 5.634632 3.173565 2 1 + 1 5.964633 6.756002 3.478956 3 1 + 8 2.874990 3.560681 4.077868 1 1 + 1 2.914829 4.534183 4.466233 2 1 + 1 1.938233 3.427028 3.627565 3 1 + 8 5.733318 11.606741 0.930065 1 1 + 1 5.579264 11.315488 12.666965 2 1 + 1 6.359242 12.394576 0.931359 3 1 + 8 1.901972 1.331481 9.115271 1 1 + 1 2.047715 1.878117 8.233836 2 1 + 1 1.131878 1.747127 9.769524 3 1 + 8 10.537506 3.176133 7.416470 1 1 + 1 11.199046 3.988586 7.363624 2 1 + 1 9.595274 3.624400 7.467070 3 1 + 8 6.989630 7.477606 2.401211 1 1 + 1 7.122337 7.303149 1.440984 2 1 + 1 7.046230 8.505044 2.601265 3 1 + 8 9.672147 8.631148 12.414566 1 1 + 1 10.551799 8.244058 12.087801 2 1 + 1 9.844583 9.533919 0.113107 3 1 + 8 1.380423 1.474473 0.850713 1 1 + 1 0.829622 2.018153 1.666538 2 1 + 1 2.212895 0.976975 1.223326 3 1 + 8 12.431363 9.775126 9.528082 1 1 + 1 12.665690 9.717969 8.525824 2 1 + 1 0.442970 10.422982 9.925529 3 1 + 8 6.036875 10.545918 10.991508 1 1 + 1 6.586134 9.764755 10.729306 2 1 + 1 5.425397 10.703740 10.253589 3 1 + 8 7.122235 11.737676 7.475741 1 1 + 1 7.059692 12.018324 6.522617 2 1 + 1 7.710331 12.407913 7.988988 3 1 + 8 4.146044 8.864820 3.244488 1 1 + 1 4.316124 7.837825 3.148160 2 1 + 1 5.002247 9.372369 3.510554 3 1 + 8 4.794503 2.508061 12.755596 1 1 + 1 4.649378 2.557791 11.796408 2 1 + 1 4.175071 1.753848 0.508864 3 1 + 8 8.617386 5.130638 10.752322 1 1 + 1 9.579710 4.705105 10.682684 2 1 + 1 7.809983 4.476989 10.596192 3 1 + 8 10.018223 11.149811 9.166402 1 1 + 1 10.737655 10.609976 9.635046 2 1 + 1 10.453338 12.008098 8.835760 3 1 + 8 11.859739 7.459123 11.429249 1 1 + 1 12.465610 8.127610 10.882785 2 1 + 1 11.608906 6.627716 10.960439 3 1 + 8 12.589836 10.011326 6.784832 1 1 + 1 11.771653 9.386968 6.725042 2 1 + 1 0.595245 9.505323 6.291081 3 1 + 8 7.103565 3.761822 2.902594 1 1 + 1 7.758703 4.610230 2.969470 2 1 + 1 7.703383 2.939273 3.130242 3 1 + 8 9.106955 6.514242 6.246590 1 1 + 1 8.800059 5.682166 6.610697 2 1 + 1 8.477858 7.253003 6.477462 3 1 + 8 1.741322 9.542076 2.275211 1 1 + 1 2.759682 9.552865 2.479834 2 1 + 1 1.482008 8.645941 1.873352 3 1 + 8 10.226237 11.347956 0.634068 1 1 + 1 11.018000 11.786599 0.137079 2 1 + 1 10.298162 11.548522 1.655512 3 1 + 8 11.388754 4.817531 10.493388 1 1 + 1 12.088434 4.138522 10.834747 2 1 + 1 11.421585 4.798596 9.466981 3 1 + 8 8.217463 9.284435 9.898369 1 1 + 1 8.986867 9.912621 9.532552 2 1 + 1 8.578968 8.833549 10.774688 3 1 + 8 7.968987 4.193506 7.416706 1 1 + 1 7.648822 3.983782 8.336825 2 1 + 1 7.148655 4.357717 6.773489 3 1 + 8 0.265608 12.657712 6.024657 1 1 + 1 12.727939 11.769066 6.525415 2 1 + 1 0.627192 12.498152 5.030983 3 1 + 8 8.298358 0.855929 9.048236 1 1 + 1 8.410791 0.465269 10.022423 2 1 + 1 9.284591 0.680646 8.656796 3 1 + 8 11.004928 1.406136 5.151804 1 1 + 1 10.531513 1.949482 5.939143 2 1 + 1 11.825807 0.947922 5.494868 3 1 + 8 2.309641 6.610263 11.687756 1 1 + 1 3.337457 6.707439 11.981482 2 1 + 1 2.151311 7.603325 11.712985 3 1 + 8 12.350244 12.572263 11.998692 1 1 + 1 0.348065 0.309654 12.657734 2 1 + 1 12.099308 0.418323 11.193882 3 1 + 8 0.555609 6.730831 1.105371 1 1 + 1 1.287509 6.273336 0.436503 2 1 + 1 12.555285 7.364645 0.634855 3 1 + 8 2.656467 4.363085 10.031849 1 1 + 1 2.378052 4.579086 9.141268 2 1 + 1 2.513117 5.273381 10.531688 3 1 + 8 4.235968 8.772504 6.696918 1 1 + 1 5.222633 8.528765 6.880275 2 1 + 1 3.795462 7.880160 6.539264 3 1 + 8 8.355265 12.485772 11.400745 1 1 + 1 7.633695 11.772047 11.162702 2 1 + 1 9.197399 12.056664 11.850959 3 1 + 8 4.936633 4.756569 1.520978 1 1 + 1 4.665780 3.854527 0.977987 2 1 + 1 5.791433 4.449838 2.001869 3 1 + 8 11.582382 7.601154 5.738973 1 1 + 1 12.040721 7.243040 4.922858 2 1 + 1 10.642139 7.328369 5.752813 3 1 + 8 4.329854 2.348348 10.121180 1 1 + 1 3.706933 1.642282 9.713293 2 1 + 1 3.832942 3.247082 10.234399 3 1 + 8 6.942708 3.148671 9.905918 1 1 + 1 5.970279 2.727750 9.785524 2 1 + 1 7.477992 2.278378 9.765477 3 1 + 8 12.034794 5.441803 7.660766 1 1 + 1 11.740226 6.436143 7.400181 2 1 + 1 0.379276 5.364141 7.725524 3 1 + 8 3.141569 12.698443 6.471658 1 1 + 1 2.800029 11.905032 6.029633 2 1 + 1 3.615808 12.345084 7.373046 3 1 + 8 0.653252 11.772559 3.322435 1 1 + 1 0.473085 12.547496 2.657823 2 1 + 1 0.900767 10.823674 2.859388 3 1 + 8 6.803150 8.710739 7.587450 1 1 + 1 7.291898 8.806543 8.477532 2 1 + 1 6.733994 9.699935 7.233150 3 1 + 8 4.215280 1.143819 4.292254 1 1 + 1 3.905948 0.636314 5.174982 2 1 + 1 3.825997 2.158234 4.355167 3 1 + 8 7.599257 7.004293 12.650324 1 1 + 1 7.693529 6.287864 11.917722 2 1 + 1 8.436650 7.582559 12.664315 3 1 + 8 2.869843 6.315534 5.417705 1 1 + 1 1.905845 6.533591 5.112560 2 1 + 1 3.665474 6.567042 4.770304 3 1 + 8 4.566786 11.118276 8.551803 1 1 + 1 4.155212 10.199371 8.091720 2 1 + 1 5.506628 11.232146 8.164216 3 1 + 8 0.259051 2.601309 3.002147 1 1 + 1 12.436242 2.090380 3.694846 2 1 + 1 12.297806 3.282948 2.638051 3 1 + 8 1.902346 4.992316 7.556653 1 1 + 1 2.339947 4.060240 7.501174 2 1 + 1 2.337986 5.463084 6.756025 3 1 + 8 1.744158 11.328245 9.812908 1 1 + 1 2.655388 11.109842 9.492455 2 1 + 1 1.642541 12.411108 9.521964 3 1 + 8 2.418084 10.314228 5.297515 1 1 + 1 3.146433 9.693256 5.257205 2 1 + 1 1.908271 10.527869 4.431857 3 1 + 8 1.594830 9.321602 11.611698 1 1 + 1 1.847416 9.861215 10.741834 2 1 + 1 1.515399 9.910609 12.375829 3 1 + 8 0.664413 6.123192 3.849919 1 1 + 1 12.433135 5.653503 4.068107 2 1 + 1 0.649610 6.194002 2.829559 3 1 + 8 10.408366 12.050090 3.310024 1 1 + 1 10.211619 12.728138 3.953735 2 1 + 1 11.367778 11.726409 3.459985 3 1 + 8 6.637013 10.017721 3.220176 1 1 + 1 6.391239 10.689026 2.508239 2 1 + 1 6.807776 10.568540 4.092530 3 1 +&END + +# Molecular dynamics parameters + +&MD +nhist 500 +preext 1.0d0 +text 298.0 +ntrialmax 100 +nrelax 1 +timestep 0.001 +ensemble npt 0.1 0.1 4.9d-5 +rcutoff 6.0 0.1 +&END + +# Force field parameters + +&FORCE +elect coul 3 +1 -0.82 +2 +0.41 +3 +0.41 +vdw 1 +1 1 lj 0.006739880631 3.165492 +&END + +# Molecules to be considered + +&MOLEC +molecs 2 +H2O 32 3 +bends 1 +2 1 3 harm 3.2913 113.24 +bonds 2 +1 2 harm 45.9296231 1.012 +1 3 harm 45.9296231 1.012 +H2O 32 3 +bends 1 +2 1 3 harm 3.2913 113.24 +bonds 2 +1 2 harm 45.9296231 1.012 +1 3 harm 45.9296231 1.012 +&END diff --git a/EXAMPLES/graphene/HICOLM.in b/EXAMPLES/graphene/HICOLM.in new file mode 100644 index 0000000..1b5c2f1 --- /dev/null +++ b/EXAMPLES/graphene/HICOLM.in @@ -0,0 +1,82 @@ +# Method to be used: Molecular dynamics or Tight-binding + +&INIT +method TB +&END + +# Unitary cell coordinates + +&CELL + 2.130000 1.229756 0.000000 + 2.130000 -1.229756 0.000000 + 0.000000 0.000000 42.600000 +&END + +# Tight-binding potential parameters + +&TBIND +diagop 2 +rcutt 2.1d0 +lcutt 0.25d0 +dens 939.6697 F +nonst 4 +0 0 T 1 -12.9323 0.0000 +1 -1 T 1 -6.5713 0.0003 +1 0 T 1 -3.9949 0.0005 +1 1 T 1 -4.2264 0.0004 +nsk 4 +0 0 0 3 T +-4.2555 0.2979 -0.1415 0.0000 ++0.0002 0.0012 -0.4923 0.0000 +0 1 0 3 T ++3.1145 -0.0016 0.0555 0.0000 +-0.0024 7.2748 0.0402 0.0000 +1 1 0 3 T ++4.4436 0.0000 0.0000 0.0000 +-0.0005 0.0000 0.0000 0.0000 +1 1 1 3 T +-2.7442 0.0080 0.0000 0.0000 ++0.0161 24.3711 0.0000 0.0000 +&END + +# orbitals to be considered + +&ORBIT +nlo 2 +0 1 0 +1 3 -1 0 1 +&END + +# K-points in the Brillouin zone for the optimizing process + +&OPTIM +nopt 1 +nkrlx 5 +1 1 6 0.00 2.13 1.64 0.50 1.50 0.30 +2 2 6 0.00 2.13 1.65 0.40 1.50 0.30 +3 3 6 0.00 2.13 1.65 0.40 1.50 0.30 +4 4 7 0.00 2.13 1.65 0.40 1.50 0.30 1.80 +5 5 3 0.00 2.13 1.65 +&END + +# atomic coordinates + +&COORD +natom 2 +6 0.00090703 0.00000000 1.00000709 1 1 +6 2.83910991 -0.00000000 1.00000010 1 1 +&END + +# Tight-binding properties + +&PROPER +prop BANDS +bandopt 2 +nband 4 +1 0.66666 0.33333 0. K +100 0.00000 0.00000 0. G +100 0.50000 0.00000 0. M +100 0.66666 0.33333 0. K +mesh 250 +kptt0 0d0 0.d0 0.d0 +&END diff --git a/README.md b/README.md new file mode 100644 index 0000000..c8d46a7 --- /dev/null +++ b/README.md @@ -0,0 +1,11 @@ +# HICOLM 1.0.0 + Multi-Methods for Molecules and Condensed Systems + + +## Reference + +If you used HICOLM in publishing results, please cite the following reference: +

F. W. Fernandes, HICOLM: High-Performance Platform of Physical Simulations by Using Low Computational Cost Methods. doi: 10.22456/2175-2745.92486.

diff --git a/SRC/MAIN/alloc_arrays.f90 b/SRC/MAIN/alloc_arrays.f90 new file mode 100644 index 0000000..b2d6f62 --- /dev/null +++ b/SRC/MAIN/alloc_arrays.f90 @@ -0,0 +1,47 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module alloc_arrays + !****************************************************************************************** + ! Alocação estática de arrays * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use input + + integer, allocatable :: bondsmlc(:),bendsmlc(:),torsmlc(:) + + real(8) strmax,str(6),cxx(6,6),exx(6),sxx(6,6) + +contains + + subroutine system_arrays + !**************************************************************************************** + ! Alocacao de variaveis globais * + !**************************************************************************************** + !-alocando arrays referentes ao Campo de Força + ! + allocate(bondsmlc(nmolec),bendsmlc(nmolec),torsmlc(nmolec)) + ! + !-alocando variaveis canonicas + ! + return + + end subroutine system_arrays + +end module alloc_arrays diff --git a/SRC/MAIN/brillouin.f90 b/SRC/MAIN/brillouin.f90 new file mode 100644 index 0000000..786e916 --- /dev/null +++ b/SRC/MAIN/brillouin.f90 @@ -0,0 +1,198 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module brillouin + !******************************************************************************************* + ! Propriedades referentes ao espaço reciproco: * + !-Distribuicao de pontos K * + !-Vetores da rede reciproca * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !******************************************************************************************* + + use sistema + use input + use estrutura + + real(8) vr(3,3),vrn(3),vzb(3,3),vzbn(3) + real(8) kxmax,kymax,kzmax,kxmin,kymin,kzmin + + save vr,vrn,kxmax,kymax,kzmax,kxmin,kymin,kzmin + +contains + + subroutine reciprocal + !**************************************************************************************** + ! Vetores da rede reciproca * + !**************************************************************************************** + + implicit none + + integer i,j + real(8) s + + !-produto vetorial ai x aj + + vr(1,1)=(v(2,2)*v(3,3)-v(2,3)*v(3,2)) + vr(1,2)=(v(2,3)*v(3,1)-v(2,1)*v(3,3)) + vr(1,3)=(v(2,1)*v(3,2)-v(2,2)*v(3,1)) + vr(2,1)=(v(3,2)*v(1,3)-v(3,3)*v(1,2)) + vr(2,2)=(v(3,3)*v(1,1)-v(3,1)*v(1,3)) + vr(2,3)=(v(3,1)*v(1,2)-v(3,2)*v(1,1)) + vr(3,1)=(v(1,2)*v(2,3)-v(1,3)*v(2,2)) + vr(3,2)=(v(1,3)*v(2,1)-v(1,1)*v(2,3)) + vr(3,3)=(v(1,1)*v(2,2)-v(1,2)*v(2,1)) + + !-volume da celula reciproca a1*(a2 x a3)/2pi + + s=0.d0 + do j=1,3 + s=s+v(1,j)*vr(1,j) + end do + + s=s/(2.d0*pi) + + !-vetores da rede reciproca + + do i=1,3 + vrn(i)=0.d0 + do j=1,3 + vr(i,j)=vr(i,j)/s + vrn(i)=vrn(i)+vr(i,j)**2 + end do + vrn(i)=sqrt(vrn(i)) + end do + + !-limites da zona de Brillouin + + kxmin=min(vr(1,1),min(vr(2,1),vr(3,1))) + kymin=min(vr(1,2),min(vr(2,2),vr(3,2))) + kzmin=min(vr(1,3),min(vr(2,3),vr(3,3))) + + kxmax=max(vr(1,1),max(vr(2,1),vr(3,1))) + kymax=max(vr(1,2),max(vr(2,2),vr(3,2))) + kzmax=max(vr(1,3),max(vr(2,3),vr(3,3))) + + !-imprimindo informaçoes do espaco reciproco + + write(6,*)('#',i=1,70) + write(6,*)'$$$$$$$$$ ',('ESPACO RECIPROCO ',i=1,3),'$$$$$$$$$' + write(6,*)('#',i=1,70) + write(6,*) + write(6,'(a16,3f15.8)')'Lattice constts:',(vrn(i)*kconv,i=1,3) + write(6,*) + write(6,'(a16,3f15.8)')'Lattice vectors:',(vr(1,i)*kconv,i=1,3) + write(6,'(16x,3f15.8)')(vr(2,i)*kconv,i=1,3) + write(6,'(16x,3f15.8)')(vr(3,i)*kconv,i=1,3) + write(6,*) + + return + + end subroutine reciprocal + + subroutine high_symmetry(oprt,lsym,nvec,n) + !**************************************************************************************** + ! Calculo dos pontos K na linha de simetria * + ! * + !-bandopt = 1 -> pi/a * + !-bandopt = 2 -> vetores internos * + !**************************************************************************************** + + implicit none + + integer i,j,l,k,n,sdband,oprt + real(8) lsym(nkmax,3),vec(nbandmax,3) + real(8) s,snvec,nvec(nbandmax),bandn(nbandmax,3) + + !-linhas de simetria na zona de brillouin + + select case(bandopt) + case(1) + do i=1,nband + bandn(i,1)=band(i,1)*1.d0*pi/(1.0d0/kconv) + bandn(i,2)=band(i,2)*1.d0*pi/(1.0d0/kconv) + bandn(i,3)=band(i,3)*1.d0*pi/(1.0d0/kconv) + end do + case(2) + do k=1,3 + do i=1,nband + bandn(i,k)=0.d0 + do l=1,3 + bandn(i,k)=bandn(i,k)+band(i,l)*vr(l,k) + end do + end do + end do + end select + + do j=1,3 + vec(1,j)=0.d0 + do i=2,nband + vec(i,j)=bandn(i,j)-bandn(i-1,j) + end do + end do + + lsym(1,1)=bandn(1,1) + lsym(1,2)=bandn(1,2) + lsym(1,3)=bandn(1,3) + + n=2 + do i=2,nband + do j=1,dband(i) + do k=1,3 + lsym(n,k)=bandn(i-1,k)+j*vec(i,k)/dband(i) + end do + n=n+1 + end do + end do + + n=n-1 + + snvec=0.d0 + sdband=dband(1) + do i=2,nband + s=0.d0 + do j=1,3 + s=s+vec(i,j)**2 + end do + nvec(i)=sqrt(s) + snvec=snvec+nvec(i) + sdband=sdband+dband(i) + end do + + nvec(1)=0.d0 + + if(oprt.eq.0)goto 1 + + !-imprimindo informacoes do espaço reciproco + + write(6,*) + write(6,'(a29)')'High-symmetry Brillouin zone!' + write(6,*) + write(6,'(a19,i15)')'Number of K-points:',sdband + write(6,*) + write(6,'(a25,3f15.8)')' length:',snvec + write(6,'(a25,3f15.8)')' Vectors:',(vec(2,j),j=1,3) + do i=3,nband + write(6,'(a25,3f15.8)')' ',(vec(i,j),j=1,3) + end do + write(6,*) + +1 return + + end subroutine high_symmetry + +end module brillouin diff --git a/SRC/MAIN/estrutura.f90 b/SRC/MAIN/estrutura.f90 new file mode 100644 index 0000000..67f0a2a --- /dev/null +++ b/SRC/MAIN/estrutura.f90 @@ -0,0 +1,367 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module estrutura + !****************************************************************************************** + ! Propriedades relacionada ao espaco real: * + ! - Definicao do grupo de simetria; * + ! - Definicao da celula unitaria; * + ! - Condicoes de contorno periódicas; * + ! - Condicoes de contorno inversa; * + ! - Convencao de minima imagem. * + ! - Impressao de variaveis canonicas em HICOLM.XSF e HICOLM.AXSF * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use sistema + use input + use alloc_arrays + + implicit none + + integer nmin(natmax,10),na(natmax),gsym + real(8) rmin(2,natmax),alpha,beta,gamma + + save nmin,rmin,gsym + +contains + + subroutine coordenadas(t1) + !*************************************************************************************** + ! Propriedades: * + ! - Definicao do grupo de simetria; * + ! - Definicao da celula unitaria; * + !*************************************************************************************** + + implicit none + + integer i,j + real(8) vl(3),t1,tf,sum + + !-imprimindo coordenadas em arquivo AXSF + + open(7,file='HICOLM.AXSF',status='unknown') + + !-contagem de tempo + + call cpu_time(t1) + + !-volume da celula unitaria + + vl(1)=(v(1,2)*v(2,3)-v(1,3)*v(2,2)) + vl(2)=(v(1,3)*v(2,1)-v(1,1)*v(2,3)) + vl(3)=(v(1,1)*v(2,2)-v(1,2)*v(2,1)) + + volume=0.d0 + do j=1,3 + volume=volume+v(3,j)*vl(j) + end do + + volume=abs(volume) + + !-angulos da celula unitaria + + sum=0.d0 + do j=1,3 + sum=sum+v(2,j)*v(3,j) + end do + alpha=acos(sum/(b*c)) + sum=0.d0 + do j=1,3 + sum=sum+v(1,j)*v(3,j) + end do + beta=acos(sum/(a*c)) + sum=0.d0 + do j=1,3 + sum=sum+v(1,j)*v(2,j) + end do + gamma=acos(sum/(a*b)) + + !-aplicando condicoes de contorno inversa + + call ccp_inv + + !-Definindo grupo de simetria + + call cell_symmetry + + !-imprimindo informacoes do espaço real + + write(6,*)('#',i=1,70) + write(6,*)'$$$$ ',('ESPACO REAL ',i=1,5),'$$$$$' + write(6,*)('#',i=1,70) + write(6,*) + write(6,'(a10,3f15.8)')'Latt ctes:',a*rconv,b*rconv,c*rconv + write(6,'(a10,3f15.8)')'Latt angs:',alpha*aconv,beta*aconv,gamma*aconv + write(6,*) + write(6,'(a10,3f15.8)')'Vectors R:',(v(1,i)*rconv,i=1,3) + write(6,'(a10,3f15.8)')' ',(v(2,i)*rconv,i=1,3) + write(6,'(a10,3f15.8)')' ',(v(3,i)*rconv,i=1,3) + write(6,*) + write(6,'(a14,f10.4)')' VOLUME:',volume*rconv**3 + write(6,*) + write(6,'(a14,i10)')' Symmetry:',gsym + + write(6,*) + + !-contagem de tempo + + call cpu_time(tf) + + t1=tf-t1 + + return + + end subroutine coordenadas + + subroutine ccp(i,j,rx,ry,rz,xvz,yvz,zvz) + !**************************************************************************************** + ! Condicoes de contorno periodicas * + !**************************************************************************************** + implicit none + + integer i,j,rx,ry,rz + real(8) xx,yy,zz,xvz,yvz,zvz + + xx=xa(j)+rx*v(1,1)+ry*v(2,1)+rz*v(3,1) + yy=ya(j)+rx*v(1,2)+ry*v(2,2)+rz*v(3,2) + zz=za(j)+rx*v(1,3)+ry*v(2,3)+rz*v(3,3) + + xvz=xx-xa(i) + yvz=yy-ya(i) + zvz=zz-za(i) + + return + + end subroutine ccp + + subroutine mic(i,j,xvz,yvz,zvz) + !*************************************************************************************** + ! Convencao de minima imagem * + !*************************************************************************************** + + implicit none + + integer i,j + real(8) xx,yy,zz,xvz,yvz,zvz + + xx=v(1,1)+v(2,1)+v(3,1) + yy=v(1,2)+v(2,2)+v(3,2) + zz=v(1,3)+v(2,3)+v(3,3) + + xvz=(xa(j)-xa(i))-xx*int(2.d0*(xa(j)-xa(i))/xx) + yvz=(ya(j)-ya(i))-yy*int(2.d0*(ya(j)-ya(i))/yy) + zvz=(za(j)-za(i))-zz*int(2.d0*(za(j)-za(i))/zz) + + return + + end subroutine mic + + subroutine ccp_inv() + !*************************************************************************************** + ! Condicoes de contorno inversa * + !*************************************************************************************** + implicit none + + integer i + real(8) xvz,yvz,zvz + + do i=1,natom + xvz=v(1,1)+v(2,1)+v(3,1) + yvz=v(1,2)+v(2,2)+v(3,2) + zvz=v(1,3)+v(2,3)+v(3,3) + xa(i)=xa(i)-xvz*nint(xa(i)/xvz) + ya(i)=ya(i)-yvz*nint(ya(i)/yvz) + za(i)=za(i)-zvz*nint(za(i)/zvz) + end do + + return + + end subroutine ccp_inv + + subroutine ccpmm(i,j,xvz,yvz,zvz) + !*************************************************************************************** + !subrotina responsavel por aplicar condicoes de contorno * + !*************************************************************************************** + + implicit none + + integer i,j,rx,ry,rz + real(8) xvz,yvz,zvz,xx,yy,zz,xvzz,yvzz,zvzz + + xvzz=xa(j)-xa(i) + yvzz=ya(j)-ya(i) + zvzz=za(j)-za(i) + + do rx=-1,1 + do ry=-1,1 + do rz=-1,1 + xx=rx*v(1,1)+ry*v(2,1)+rz*v(3,1) + yy=rx*v(1,2)+ry*v(2,2)+rz*v(3,2) + zz=rx*v(1,3)+ry*v(2,3)+rz*v(3,3) + xvz=xvzz-xx*aint(2.d0*xvzz/xx) + yvz=yvzz-yy*aint(2.d0*yvzz/yy) + zvz=zvzz-zz*aint(2.d0*zvzz/zz) + end do + end do + end do + + return + + end subroutine ccpmm + + subroutine cell_symmetry + !*************************************************************************************** + ! Grupos de simetria * + !*************************************************************************************** + + implicit none + + real(8) prec + + !-definindo precisão + + prec=1.d-2 + + if(gsymopt.eq.0)goto 1 + + gsym=gsymopt + + goto 2 + + !-triclinico + +1 gsym=1 + + !-cubico + + if(abs(2.d0*alpha-pi).le.prec)then + if(abs(2.d0*beta-pi).le.prec)then + if(abs(2.d0*gamma-pi).le.prec)then + if(abs(a-b).le.prec)then + if(abs(a-c).le.prec)gsym=23 + end if + end if + end if + end if + + !-Hexagonal + + if(abs(2.d0*alpha-acos(-1.d0)).le.prec)then + if(abs(2.d0*beta-acos(-1.d0)).le.prec)then + if(abs(a-b).le.prec)then + if(abs(2.d0*gamma-pi/6.d0).le.prec.or.& + abs(2.d0*gamma-pi/3.d0).le.prec)gsym=6 + end if + end if + end if + +2 return + + end subroutine cell_symmetry + + subroutine geometria() + !*************************************************************************************** + ! - Impressao de variaveis canonicas em HICOLM.XSF * + !*************************************************************************************** + + implicit none + + integer i,k,j + + !-abrindo ficheiro + + open(1,file='HICOLM.XSF',status='unknown') + + !-imprimindo arquivo XSF + + write(1,*)'BEGIN_INFO' + write(1,*)' #' + write(1,*)' # This is a XCRYSDEN-Structure-File' + write(1,*)' # aimed for Visualization of Fermi Surface' + write(1,*)' #' + write(1,*)' # Case: Tight-binding calculation' + write(1,*)' #' + write(1,*)' # Launch as: xcrysden --xsf HICOLM.XSF' + write(1,*)' #' + write(1,*)'END_INFO' + + k=1 + + write(1,*)'# estrutura final' + write(1,'(a7)')'CRYSTAL' + + write(1,'(a7)')'PRIMVEC' + do i=1,3 + write(1,'(3(3x,f14.8))')(v(i,j)*rconv,j=1,3) + end do + + write(1,'(a9)')'PRIMCOORD' + write(1,'(2i5)')natom,k + + do i=1,natom + write(1,'(i5,3f14.8,2x,3f14.8,2x,3f14.8)') & + idna(i),xa(i)*rconv,ya(i)*rconv,za(i)*rconv, & + fax(i)*econv/rconv,fay(i)*econv/rconv,faz(i)*econv/rconv, & + vax(i)*rconv/tconv,vay(i)*rconv/tconv,vaz(i)*rconv/tconv + end do + + close(1) + + return + + end subroutine geometria + + subroutine history(ihist) + !*************************************************************************************** + ! Impressao de variaveis canonicas por frame em HICOLM.AXSF * + !*************************************************************************************** + + implicit none + + integer i,j,k,ihist + real(8) fnorm + + k=1 + + if(ihist.eq.1)then + write(7,*)'# Historico de coordenadas' + write(7,'(a9,i5)')'ANIMSTEPS',int((ntrialmax-nrelax)/nhist) + write(7,'(a7)')'CRYSTAL' + end if + + write(7,'(a7,i5)')'PRIMVEC',ihist + do i=1,3 + write(7,'(3(3x,f14.8))')(v(i,j)*rconv,j=1,3) + end do + write(7,'(a9,i5)')'PRIMCOORD',ihist + write(7,'(2i5)')natom,k + + do i=1,natom + fnorm=sqrt(fax(i)**2+fay(i)**2+faz(i)**2)*econv/rconv + write(7,'(i5,7f14.8)')idna(i),xa(i)*rconv,ya(i)*rconv,za(i)*rconv,& + fax(i)*econv/rconv,fay(i)*econv/rconv,faz(i)*econv/rconv,fnorm + end do + + ihist=ihist+1 + + return + + end subroutine history + +end module estrutura diff --git a/SRC/MAIN/input.f90 b/SRC/MAIN/input.f90 new file mode 100644 index 0000000..4f85e2a --- /dev/null +++ b/SRC/MAIN/input.f90 @@ -0,0 +1,1320 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module input + !**************************************************************************************** + ! Leitura dos dados de entrada * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !**************************************************************************************** + + use sistema + + implicit none + !---------------------------------------------------------------------------- + !-constantes + ! + real(8) pi,rconv,econv,kconv,pconv,aconv,mconv,tconv,teconv,hcconv + real(8) elconv,keconv,n0,kb,kelect + ! + complex(8) img + character(7) method + ! + save rconv,econv,pconv,kconv,aconv,mconv,tconv,teconv,hcconv,elconv,keconv + save kb,pi,img,n0 + !---------------------------------------------------------------------------- + !-variaveis de estrutura + integer rxmx,rymx,rzmx,gsymopt,natom,reuse,idna(natmax) + ! + real(8) a,b,c,xa(natmax),ya(natmax),za(natmax),v(3,3),volume + real(8) vax(natmax),vay(natmax),vaz(natmax),fax(natmax),fay(natmax),faz(natmax) + ! + save rxmx,rymx,rzmx,gsymopt,natom,reuse,idna + !---------------------------------------------------------------------------- + !-variaveis da mecanica molecular + integer nhist,ntrialmax,nrelax,nxmolec(molecmax),bendscnt(molecmax),bondscnt(molecmax) + integer atp(natmax),ato(natmax),fztp(natmax),nrl,atnp(ntpmax),natnp(ntpmax) + integer vdw(ntpmax,ntpmax),bonds(molecmax,bondmax),bends(molecmax,bendmax),tersoff + integer tors(molecmax,torsmax),molbend(molecmax,bendmax,3),torscnt(molecmax) + integer dstp,ndstp,xstp,nmolec,moltot,nfree,spctot,molbond(molecmax,bondmax,2) + integer nvdw,nbonds,nbends,ncoul,ntrsff,ntors,moltors(molecmax,torsmax,4) + ! + real(8) dtime,drmax,fmstp,text,tstat,preext,pstat,bfactor,lrmax,fzstr(6) + real(8) parbnd(molecmax,bondmax,5),parvdw(ntpmax,ntpmax,3) + real(8) parbend(molecmax,bendmax,4),parcoul(ntpmax,1),partrsff(ntpmax,ntpmax,16) + real(8) partors(molecmax,torsmax,2) + real(8) mass(natmax),massmin,massmax,rcutoff,drcutoff,lambdain,lambdafi + ! + character(2) att + character(7) prop,ensble + character(7) coulop + character(10) namemol(molecmax) + ! + save dtime,drmax,nhist,ntrialmax,nrelax,nxmolec,fmstp,dstp,xstp,ndstp,drcutoff + save mass,massmin,massmax,prop,namemol,nmolec,moltot,nfree,spctot,ensble,rcutoff + save att,atp,ato,nrl,fztp,atnp,natnp,text,preext,pstat,bfactor,tstat,lrmax,fzstr + save parbnd,parvdw,parbend,parcoul,partrsff,lambdain,lambdafi,partors + save vdw,bonds,bends,nvdw,nbonds,nbends,ncoul,ntrsff,ntors,coulop,tersoff,tors + save bendscnt,molbend,bondscnt,molbond,torscnt + !---------------------------------------------------------------------------- + !-variaveis do método Tight-binding + integer ntype,ntmolec(molecmax),nzmolec(molecmax),mmop(lmax,mmax) + integer nskpar,nlopar,mlop(lmax),mesh,nband,diagop,bandopt,msk(nparammax),mskt(nparammax) + integer nprllm(nparammax),npril(lmax,mmax),mpack(3),ebndtot,dband(5),mmopar(lmax) + integer nlo,lo(lmax),mo(lmax,mmax),mlo(mmax),norb,nonst,nparam,nparamt + integer dkrlx(nkrlxmax),nrlx(nkrlxmax),ntblx(nkrlxmax),nkrlx,nopt,lfermi + ! + real(8) band(nbandmax,3),lcutt,rcutt,err,spr(lmax),onst0(lmax,mmax,nprllmmax) + real(8) fermi,ksh(3),tpr0(nparammax,nprllmmax),spr0(nparammax,nprllmmax) + real(8) dens0,kptt0(3),krlx(nkrlxmax,dkrlxmax) + ! + logical chk(nparammax),chko(lmax,mmax),chkden + ! + save ntype,ntmolec,nzmolec + save nskpar,nlopar,mlop,mesh,nband,diagop,bandopt,chk,chko,chkden,lfermi + save nprllm,npril,mpack,ebndtot,nlo,lo,mo,mlo,norb,nonst,nparam,nparamt,msk + save band,lcutt,rcutt,err,spr,ksh,kptt0,nopt,dkrlx,nrlx,ntblx,nkrlx,krlx + !--------------------------------------------------------------------------- +contains + + subroutine entrada(t0) + !*************************************************************************************** + ! Leitura dos parametros de entrada * + !*************************************************************************************** + implicit none + + integer i,j + real(8) val(20),t0,tf + character(7) in,char + character(9) key + + open(5,file='HICOLM.in',status='old') + + !-contagem de tempo + + call cpu_time(t0) + + !-atribuindo valores default + + call default + + !-Escolha do metodo + +1 read(5,*,end=11)in + + if(in.ne.'&INIT')goto 1 + + do i=1,100 + read(5,*)key + if(key.eq.'&END')exit + backspace(5) + read(5,*)key,char + if(key.eq.'method')method=char + end do + +11 rewind(5) + +2 read(5,*,end=22)in + + !-Parametros de rede + + if(in.ne.'&CELL')goto 2 + + do i=1,3 + read(5,*)(v(i,j),j=1,3) + end do + + !-base + +22 rewind(5) + +3 read(5,*,end=33)in + + if(in.ne.'&COORD')goto 3 + + do i=1,100 + read(5,*)key + if(key.eq.'&END')exit + backspace(5) + read(5,*)key,val(1) + if(key.eq.'reuse')reuse=int(val(1)) + if(key.eq.'gsymopt')gsymopt=int(val(1)) + if(key.eq.'err')err=val(1) + if(key.eq.'replc')then + backspace(5) + read(5,*)key,rxmx,rymx,rzmx + end if + if(key.eq.'natom')then + backspace(5) + read(5,*)key,val(1) + natom=int(val(1)) + do j=1,natom + read(5,*)idna(j),xa(j),ya(j),za(j),atp(j),fztp(j) + end do + end if + end do + +33 rewind(5) + + select case(method) + case('TB') + call tb_input +! rewind(5) + case('MD') + call md_input + end select + + !-convertendo unidades de medida + + call convert + + !-contagem de tempo + + call cpu_time(tf) + + t0=tf-t0 + + return + + end subroutine entrada + + subroutine tb_input + !*************************************************************************************** + ! Leitura dos parametros de entrada do metodo Tight-binding * + !*************************************************************************************** + implicit none + + integer i,j,k,m,l1,l2,m1,nsk + real(8) val(20) + character(7) in,char + character(9) key + logical loc + + !-parametros para o calculo tight-binding + +1 read(5,*,end=11)in + + if(in.ne.'&TBIND')goto 1 + + do i=1,100 + read(5,*)key + if(key.eq.'&END')exit + backspace(5) + read(5,*)key,val(1) + if(key.eq.'diagop')diagop=int(val(1)) + if(key.eq.'rcutt')rcutt=val(1) + if(key.eq.'lcutt')lcutt=val(1) + if(key.eq.'dens')then + backspace(5) + read(5,*)key,val(1),loc + dens0=val(1) + chkden=loc + end if + if(key.eq.'nonst')then + backspace(5) + read(5,*)key,val(1) + nonst=int(val(1)) + do j=1,nonst + read(5,*)l1,m1,loc,val(1) + m1=m1+(l1+1) + l1=l1+1 + chko(l1,m1)=loc + npril(l1,m1)=int(val(1)) + backspace(5) + read(5,*)val(1),val(1),loc,val(1),(onst0(l1,m1,k),k=1,npril(l1,m1)) + end do + end if + if(key.eq.'nsk')then + backspace(5) + read(5,*)key,val(1) + nsk=int(val(1)) + do j=1,nsk + read(5,*)l1,l2,m1,val(1),loc + call labels(l1+1,l2+1,m1+1,m) + nprllm(m)=int(val(1)) + read(5,*)(tpr0(m,k),k=1,nprllm(m)) + read(5,*)(spr0(m,k),k=1,nprllm(m)) + chk(m)=loc + end do + end if + end do + + !-definindo parametros para o fitting + +11 rewind(5) + +2 read(5,*,end=22)in + + if(in.ne.'&OPTIM')goto 2 + + do i=1,100 + read(5,*)key + if(key.eq.'&END')exit + backspace(5) + read(5,*)key,val(1) + if(key.eq.'nopt')nopt=int(val(1)) + if(key.eq.'nkrlx')then + backspace(5) + read(5,*)key,val(1) + nkrlx=int(val(1)) + do j=1,nkrlx + read(5,*)ntblx(j),nrlx(j),dkrlx(j) + backspace(5) + read(5,*)ntblx(j),nrlx(j),dkrlx(j),(krlx(j,k),k=1,dkrlx(j)) + end do + end if + end do + + !-momento angular e orbitais atomicos + +22 rewind(5) + +3 read(5,*,end=33)in + + if(in.ne.'&ORBIT')goto 3 + + do i=1,100 + read(5,*)key + if(key.eq.'&END')exit + if(key.eq.'nlo')then + backspace(5) + read(5,*)key,val(1) + nlo=int(val(1)) + do k=1,nlo + read(5,*)lo(k),mlo(k) + backspace(5) + read(5,*)val(1),val(2),(mo(k,j),j=1,mlo(k)) + end do + end if + end do + + !-propriedades do metodo tight-binding + +33 rewind(5) + +4 read(5,*,end=44)in + + if(in.ne.'&PROPER')goto 4 + + do i=1,100 + read(5,*)key + if(key.eq.'&END')exit + if(key.eq.'prop')then + backspace(5) + read(5,*)key,char + prop=char + end if + if(key.eq.'bandopt')then + backspace(5) + read(5,*)key,val(1) + bandopt=int(val(1)) + end if + if(key.eq.'nband')then + backspace(5) + read(5,*)key,val(1) + nband=int(val(1)) + do j=1,nband + read(5,*)dband(j),(band(j,k),k=1,3) + end do + end if + if(key.eq.'mesh')then + backspace(5) + read(5,*)key,val(1) + mesh=int(val(1)) + end if + if(key.eq.'fermi')then + backspace(5) + read(5,*)key,val(1) + fermi=int(val(1)) + end if + if(key.eq.'lfermi')then + backspace(5) + read(5,*)key,val(1) + lfermi=int(val(1)) + end if + if(key.eq.'kptt0')then + backspace(5) + read(5,*)key,(kptt0(j),j=1,3) + end if + end do + + !-calculando qtdes de parametros e orbitais atomicos + +44 norb=0 + do i=1,nlo + do j=1,mlo(i) + norb=norb+1 + end do + end do + + norb=norb*natom + + do i=1,nlo + do j=1,mlo(i) + mo(i,j)=mo(i,j)+(lo(i)+1) + end do + lo(i)=lo(i)+1 + end do + + nlopar=0 + do i=1,nlo + mmopar(nlopar+1)=0 + do j=1,mlo(i) + if(chko(lo(i),mo(i,j)).eqv..true..and.chko(lo(i),mo(i,j)).neqv..false.)& + then + mlop(nlopar+1)=lo(i) + mmop(nlopar+1,mmopar(nlopar+1)+1)=mo(i,j) + mmopar(nlopar+1)=mmopar(nlopar+1)+1 + end if + end do + nlopar=nlopar+1 + end do + + nskpar=0 + nparamt=0 + do i=1,nlo + do j=i,nlo + l1=min(lo(i),lo(j)) + l2=max(lo(i),lo(j)) + do k=1,l1 + call labels(l1,l2,k,m) + if(m.ne.0)then + if(chk(m).eqv..true..and.chk(m).neqv..false.)then + msk(nskpar+1)=m + nskpar=nskpar+1 + end if + mskt(nparamt+1)=m + nparamt=nparamt+1 + end if + end do + end do + end do + + nparam=0 + + if(chkden.eqv..true.)nparam=nparam+1 + + do i=1,nlopar + do j=1,mmopar(i) + nparam=nparam+npril(mlop(i),mmop(i,j)) + end do + end do + do i=1,nskpar + nparam=nparam+2*nprllm(msk(i)) + end do + + return + + end subroutine tb_input + + subroutine md_input + !*************************************************************************************** + ! Leitura dos parametros de entrada da Dinamica molecular * + !*************************************************************************************** + implicit none + + integer i,j,k,g,p,m,numt,natfx + real(8) val(20) + character(7) in,char + character(9) key + + !-parametros de dinâmica molecular + +1 read(5,*,end=11)in + + if(in.ne.'&MD')goto 1 + + do i=1,100 + read(5,*)key + if(key.eq.'&END')exit + if(key.eq.'nhist')then + backspace(5) + read(5,*)key,val(1) + nhist=int(val(1)) + end if + if(key.eq.'ntrialmax')then + backspace(5) + read(5,*)key,val(1) + ntrialmax=int(val(1)) + end if + if(key.eq.'rcutoff')then + backspace(5) + read(5,*)key,val(1),val(2) + rcutoff=val(1) + drcutoff=val(2) + end if + if(key.eq.'timestep')then + backspace(5) + read(5,*)key,val(1) + dtime=val(1) + end if + if(key.eq.'drmax')then + backspace(5) + read(5,*)key,(val(j),j=1,5) + drmax=val(1) + fmstp=val(2) + dstp=int(val(3)) + ndstp=int(val(4)) + xstp=int(val(5)) + end if + if(key.eq.'lambda')then + backspace(5) + read(5,*)key,(val(j),j=1,2) + lambdain=val(1) + lambdafi=val(2) + end if + if(key.eq.'tstat')then + backspace(5) + read(5,*)key,val(1) + tstat=val(1) + end if + if(key.eq.'text')then + backspace(5) + read(5,*)key,val(1) + text=val(1) + end if + if(key.eq.'preext')then + backspace(5) + read(5,*)key,val(1) + preext=val(1) + end if + if(key.eq.'pstat')then + backspace(5) + read(5,*)key,val(1),val(2) + pstat=val(1) + bfactor=val(2) + end if + if(key.eq.'ensemble')then + backspace(5) + read(5,*)key,char + if(char.eq.'nve')then + ensble=char + elseif(char.eq.'nvt')then + backspace(5) + read(5,*)key,char,val(1) + tstat=val(1) + ensble=char + elseif(char.eq.'npt')then + backspace(5) + read(5,*)key,char,val(1),val(2),val(3) + tstat=val(1) + pstat=val(2) + bfactor=val(3) + ensble=char + end if + end if + if(key.eq.'fzstr')then + backspace(5) + read(5,*)key,(val(j),j=1,6) + do j=1,6 + fzstr(j)=val(j) + end do + end if + end do + + !-Campo de Forca + +11 rewind(5) + +2 read(5,*,end=22)in + + if(in.ne.'&FORCE')goto 2 + + do i=1,100 + read(5,*)key + if(key.eq.'&END')exit + if(key.eq.'ebndtot')then + backspace(5) + read(5,*)key,val(1) + ebndtot=int(val(1)) + end if + if(key.eq.'vdw')then + backspace(5) + read(5,*)key,nvdw + do j=1,nvdw + read(5,*)val(1),val(2),char + call vdw_opt(char,m,numt) + backspace(5) + read(5,*)val(1),val(2),char,(val(k),k=3,2+numt) + do k=1,numt + parvdw(int(val(1)),int(val(2)),k)=val(k+2) + parvdw(int(val(2)),int(val(1)),k)=val(k+2) + end do + vdw(int(val(1)),int(val(2)))=m + vdw(int(val(2)),int(val(1)))=m + end do + end if + if(key.eq.'elect')then + backspace(5) + read(5,*)key,char,ncoul + do j=1,ncoul + call coul_opt(char,numt) + read(5,*)(val(k),k=1,numt+1) + do k=1,numt + parcoul(int(val(1)),k)=val(k+1) + end do + end do + coulop=char + end if + if(key.eq.'tersoff')then + backspace(5) + read(5,*)key,char,ntrsff + call trsff_opt(char,m,numt) + do j=1,ntrsff + read(5,*)(val(k),k=1,numt+2) + do k=1,numt + partrsff(int(val(1)),int(val(2)),k)=val(k+2) + partrsff(int(val(2)),int(val(1)),k)=val(k+2) + end do + tersoff=m + end do + end if + end do + + !-Descricao das moleculas por especie + +22 rewind(5) + +3 read(5,*,end=33)in + + if(in.ne.'&MOLEC')goto 3 + + do i=1,100 + read(5,*)key + if(key.eq.'&END')exit + if(key.eq.'molecs')then + backspace(5) + read(5,*)key,nmolec + do j=1,nmolec + read(5,*)namemol(j),ntmolec(j),nxmolec(j) + do g=1,3 + read(5,*)key + if(key.eq.'&END')goto 33 + if(key.eq.'bends')then + backspace(5) + read(5,*)key,bendscnt(j) + do k=1,bendscnt(j) + read(5,*)val(1),val(2),val(3),char + call bend_opt(char,m,numt) + backspace(5) + read(5,*)val(1),val(2),val(3),char,(val(p),p=4,3+numt) + do p=1,numt + parbend(j,k,p)=val(p+3) + end do + bends(j,k)=m + molbend(j,k,1)=int(val(1)) + molbend(j,k,2)=int(val(2)) + molbend(j,k,3)=int(val(3)) + end do + elseif(key.eq.'bonds')then + backspace(5) + read(5,*)key,bondscnt(j) + do k=1,bondscnt(j) + read(5,*)val(1),val(2),char + call bonds_opt(char,m,numt) + backspace(5) + read(5,*)val(1),val(2),char,(val(p),p=3,2+numt) + do p=1,numt + parbnd(j,k,p)=val(p+2) + end do + bonds(j,k)=m + molbond(j,k,1)=int(val(1)) + molbond(j,k,2)=int(val(2)) + end do + elseif(key.eq.'dihedral')then + backspace(5) + read(5,*)key,torscnt(i) + do k=1,torscnt(i) + read(5,*)val(1),val(2),val(3),val(4),char + call dihedral_opt(char,m,numt) + backspace(5) + read(5,*)val(1),val(2),val(3),val(4),char,(val(p),p=5,4+numt) + do p=1,numt + partors(j,k,p)=val(p+4) + end do + tors(j,k)=m + moltors(j,k,1)=int(val(1)) + moltors(j,k,2)=int(val(2)) + moltors(j,k,3)=int(val(3)) + moltors(j,k,4)=int(val(4)) + end do + end if + end do + backspace(5) + end do + end if + end do + + !-calculando moleculas totais + +33 moltot=1 + do i=1,nmolec + do j=1,ntmolec(i) + nzmolec(moltot)=nxmolec(i) + moltot=moltot+1 + end do + end do + + moltot=moltot-1 + + !-calculando parametros intramoleculares totais + + nbends=0 + nbonds=0 + ntors=0 + do i=1,nmolec + do j=1,ntmolec(i) + nbends=nbends+bendscnt(i) + nbonds=nbonds+bondscnt(i) + ntors=ntors+torscnt(i) + end do + end do + + !-calculando total de especies + + atnp(1)=atp(1) + + spctot=1 + do i=2,natom + do j=1,spctot + if(atp(i).eq.atnp(j))goto 553 + end do + atnp(spctot+1)=atp(i) + spctot=spctot+1 +553 continue + end do + + do j=1,spctot + natnp(j)=0 + end do + + do i=1,natom + do j=1,spctot + if(atp(i).eq.atnp(j))natnp(j)=natnp(j)+1 + end do + end do + + !-calculando graus de liberdade + + natfx=0 + do i=1,natom + if(fztp(i).eq.0)natfx=natfx+1 + end do + + nfree=3*(natom-natfx-1) + + !-redefinindo parametros de rede e posicoes atomicas + + if(reuse.eq.1)call frame + + !-definindo massa atomica + + call atomic_mass + + return + + end subroutine md_input + + subroutine default + !*************************************************************************************** + ! Valores padrão * + !*************************************************************************************** + + implicit none + + integer i,j,k,l1,l2 + + prop='NONE' + mesh=1 + + nhist=1 + text=273.d0 + tstat=0.5d0 + pstat=0.5d0 + bfactor=4.679d-5 + preext=1.d0 + ntrialmax=1 + nrelax=1 + drmax=0.d0 + fmstp=0.d0 + ndstp=0 + dstp=0 + xstp=0 + lrmax=0.d0 + nrl=2 + + chkden=.false. + + lambdain=0.d0 + lambdafi=1.d0 + + ensble='nve' + + rcutoff=0.d0 + drcutoff=0.d0 + + reuse=0 + + gsymopt=0 + + nbonds=0 + nbends=0 + nvdw=0 + ncoul=0 + ntrsff=0 + ntors=0 + + ebndtot=0 + + coulop='coul' + + nmolec=0 + natom=0 + + rxmx=1 + rymx=1 + rzmx=1 + + tersoff=0 + + do i=1,molecmax + do j=1,torsmax + do k=1,2 + partors(i,j,k)=0.d0 + end do + tors(i,j)=0 + moltors(i,j,1)=0 + moltors(i,j,2)=0 + moltors(i,j,3)=0 + moltors(i,j,4)=0 + end do + do j=1,bendmax + do k=1,4 + parbend(i,j,k)=0.d0 + end do + bends(i,j)=0 + molbend(i,j,1)=0 + molbend(i,j,2)=0 + molbend(i,j,3)=0 + end do + do j=1,bondmax + do k=1,5 + parbnd(i,j,k)=0.d0 + end do + bonds(i,j)=0 + molbond(i,j,1)=0 + molbond(i,j,2)=0 + end do + bendscnt(i)=0 + bondscnt(i)=0 + torscnt(i)=0 + end do + + do i=1,ntpmax + do j=1,ntpmax + do k=1,16 + partrsff(i,j,k)=0.d0 + end do + do k=1,3 + parvdw(i,j,k)=0.d0 + end do + end do + parcoul(i,1)=0.d0 + end do + + do i=1,3 + kptt0(i)=0.d0 + mpack(i)=8 + ksh(i)=0.d0 + end do + + a=0.d0 + b=0.d0 + c=0.d0 + att='C' + + do i=1,natmax + xa(i)=0.d0 + ya(i)=0.d0 + za(i)=0.d0 + atp(i)=0 + fztp(i)=1 + end do + + nfree=0 + + fermi=0.d0 + + lfermi=1 + + err=0.3d0 + + bandopt=1 + + diagop=1 + + ntype=1 + + dens0=0.d0 + + lcutt=0.15d0 + + rcutt=4.d0 + + nlo=3 + do i=1,nlo + lo(i)=i + do j=1,lo(i) + mo(i,j)=j + end do + end do + + norb=0 + do i=1,nlo + do j=1,lo(i) + norb=norb+2*j-1 + end do + end do + + norb=norb*natmax + + nskpar=0 + do i=1,nlo + do j=i,nlo + nskpar=nskpar+max(lo(i),lo(j)) + end do + end do + + do i=1,nlo + do j=i+1,nlo + l1=min(lo(i),lo(j)) + l2=max(lo(i),lo(j)) + l1=l1-1 + l2=l2-1 + if(l1.eq.0.and.l2.eq.1)nskpar=nskpar-1 + if(l1.eq.0.and.l2.eq.2)nskpar=nskpar-2 + if(l1.eq.1.and.l2.eq.2)nskpar=nskpar-1 + end do + do j=1,2*i+1 + spr(i)=1.d0 + chko(i,j)=.false. + npril(i,j)=1 + do k=1,npril(i,j) + onst0(i,j,k)=0.d0 + end do + end do + k=k+2*i-1 + end do + + nparam=2*nskpar+nlo+1 + + do i=1,nskpar + do j=1,nprllmmax + tpr0(i,j)=0.d0 + spr0(i,j)=0.d0 + end do + nprllm(i)=1 + chk(i)=.false. + end do + + do i=1,6 + fzstr(i)=1.d0 + end do + + !-parametros da Dinâmica Molecular + + dtime=0.0d0 + + !-variaveis canonicas + + do i=1,natmax + vax(i)=0.d0 + vay(i)=0.d0 + vaz(i)=0.d0 + fax(i)=0.d0 + fay(i)=0.d0 + faz(i)=0.d0 + end do + + return + + end subroutine default + + subroutine convert + !************************************************************************************** + ! Conversão para o sistema padrão u.a. de unidades * + !************************************************************************************** + + implicit none + + integer i,j + + !-unidades fundamentais (SI) + + mconv=9.10938291d-31 ! massa (kg) + aconv=180.d0/acos(-1.d0) ! ângulo (radianos) + hcconv=1.054571726d-34 ! Constante de Planck (J*s). + elconv=1.602176565d-19 ! carga eletrica (C) + keconv=8.9875517873681d+9 ! constante eletrostática (N*m^2/C^2) + + !-unidades derivadas (SI) + + econv=mconv*elconv**4*keconv**2/hcconv**2 ! energia (J) + rconv=hcconv**2/(mconv*keconv*elconv**2) ! comprimento (m) + pconv=econv/rconv**3 ! pressao (N/m^2) + tconv=hcconv/econv ! tempo (s) + teconv=econv/kb ! temperatura (K) + + !-convertendo unidades SI para unidades de entrada + + mconv=mconv*(1.d+3*n0) !OK + rconv=rconv*(1.d+10) !OK + kconv=1.d0/rconv !OK + econv=econv*(6.241506363094d+18) !OK + pconv=pconv*(0.9872d-5) !OK + tconv=tconv*(1.d+12) !OK + elconv=1.d0 !OK + teconv=teconv*(6.241506363094d+18) !OK + + !-vetores de rede e coordenadas atomicas + + do i=1,3 + do j=1,3 + v(i,j)=v(i,j)/rconv + end do + end do + + a=sqrt(v(1,1)**2+v(1,2)**2+v(1,3)**2) + b=sqrt(v(2,1)**2+v(2,2)**2+v(2,3)**2) + c=sqrt(v(3,1)**2+v(3,2)**2+v(3,3)**2) + + do i=1,natom + xa(i)=xa(i)/rconv + ya(i)=ya(i)/rconv + za(i)=za(i)/rconv + end do + + !-velocidades + + do i=1,natom + vax(i)=vax(i)/(rconv/tconv) + vay(i)=vay(i)/(rconv/tconv) + vaz(i)=vaz(i)/(rconv/tconv) + end do + + !-forcas + + do i=1,natom + fax(i)=fax(i)/(econv/rconv) + fay(i)=fay(i)/(econv/rconv) + faz(i)=faz(i)/(econv/rconv) + end do + + !-parametros da Dinâmica Molecular + + drmax=drmax/rconv + preext=preext/pconv + text=text/teconv + fmstp=fmstp/(econv/rconv) + kb=kb/econv + + dtime=dtime/tconv + tstat=tstat/tconv + pstat=pstat/tconv + bfactor=bfactor*pconv + rcutoff=rcutoff/rconv + drcutoff=drcutoff/rconv + + !-parametros do Campo de Forca + + kelect=kelect/keconv + + !-unidades de massa atomica + + do i=1,natom + mass(i)=mass(i)/mconv + end do + massmin=massmin/mconv + massmax=massmax/mconv + + return + + end subroutine convert + + subroutine labels(l1,l2,m1,i) + !*************************************************************************************** + ! Parametros Slater-Koster * + !*************************************************************************************** + + implicit none + + integer l1,l2,la,lb,m1,i,ma + + i=0 + + la=min(l1,l2) + lb=max(l1,l2) + + la=la-1 + lb=lb-1 + ma=m1-1 + + if(la.eq.0)then + if(lb.eq.0)then + if(ma.eq.0)i=1 + elseif(lb.eq.1)then + if(ma.eq.0)i=2 + elseif(lb.eq.2)then + if(ma.eq.0)i=3 + end if + elseif(la.eq.1)then + if(lb.eq.1)then + if(ma.eq.0)i=4 + if(ma.eq.1)i=5 + elseif(lb.eq.2)then + if(ma.eq.0)i=6 + if(ma.eq.1)i=7 + end if + elseif(la.eq.2)then + if(lb.eq.2)then + if(ma.eq.0)i=8 + if(ma.eq.1)i=9 + if(ma.eq.2)i=10 + end if + end if + + return + + end subroutine labels + + subroutine cte + !*************************************************************************************** + ! Constantes essenciais * + !*************************************************************************************** + implicit none + + img=dcmplx(0.d0,1.d0) ! numero imaginario + pi=acos(-1.d0) ! Pi + kelect=1.d0 ! constante eletrostática + n0=6.022d+23 ! numero de Avogadro + kb=8.6173324d-5 ! constante de Boltzmann + + return + + end subroutine cte + + subroutine frame + !*************************************************************************************** + ! Leitura do ficheiro de entrada: * + ! - Coordenadas espaciais; * + ! - Velocidades; * + ! - Forca. * + !*************************************************************************************** + implicit none + + integer i,j + + open(1,file='HICOLM.XSF',status='old') + + do i=1,13 + read(1,*) + end do + + do i=1,3 + read(1,'(3(3x,f14.8))')(v(i,j),j=1,3) + end do + + read(1,*) + read(1,*)natom + + do i=1,natom + read(1,'(i5,3f14.8,2(2x,3f14.8))') & + idna(i),xa(i),ya(i),za(i),fax(i),fay(i),faz(i),vax(i),vay(i),vaz(i) + end do + + !-fechando arquivo XSF com as coordenadas atomicas + + close(1) + + return + + end subroutine frame + + subroutine vdw_opt(char,m,nprvdw) + !*************************************************************************************** + ! Flags do potencial de Van der Waals * + !*************************************************************************************** + implicit none + + integer nprvdw,m + character(7) char + + select case(char) + case('mors') + m=1 + nprvdw=3 + case('lj') + m=2 + nprvdw=2 + end select + + return + + end subroutine vdw_opt + + subroutine trsff_opt(char,m,nprtrsff) + !*************************************************************************************** + ! Flags do potencial Tersoff * + !*************************************************************************************** + implicit none + + integer nprtrsff,m + character(7) char + + select case(char) + case('ters') + nprtrsff=10 + m=1 + end select + + return + + end subroutine trsff_opt + + subroutine coul_opt(char,nprcoul) + !*************************************************************************************** + ! Flags do potencial eletrostatico * + !*************************************************************************************** + implicit none + + integer nprcoul + character(7) char + + select case(char) + case('coul') + nprcoul=1 + case('escl') + nprcoul=1 + end select + + return + + end subroutine coul_opt + + subroutine dihedral_opt(char,m,nprtors) + !*************************************************************************************** + ! Flags do potencial intramolecular de torsao * + !*************************************************************************************** + implicit none + + integer nprtors,m + character(7) char + + select case(char) + case('harm') + m=1 + nprtors=2 + end select + + return + + end subroutine dihedral_opt + + subroutine bend_opt(char,m,nprbend) + !*************************************************************************************** + ! Flags do potencial intramolecular de deformacao * + !*************************************************************************************** + implicit none + + integer nprbend,m + character(7) char + + select case(char) + case('harm') + m=1 + nprbend=2 + end select + + return + + end subroutine bend_opt + + subroutine bonds_opt(char,m,nprpar) + !*************************************************************************************** + ! Flags do potencial intramolecular de estiramento * + !*************************************************************************************** + implicit none + + integer nprpar,m + character(7) char + + select case(char) + case('mors') + m=1 + nprpar=3 + case('harm') + m=2 + nprpar=2 + end select + + return + + end subroutine bonds_opt + + subroutine atomic_mass + !*************************************************************************************** + ! Massas atomicas * + !*************************************************************************************** + implicit none + + integer i + + !-definindo massa atomica + + do i=1,natom + select case(idna(i)) + case(1) + mass(i)=1.00794d0 + case(6) + mass(i)=12.0107d0 + case(7) + mass(i)=14.0067d0 + case(8) + mass(i)=15.9994d0 + case(18) + mass(i)=39.9480d0 + case(80) + mass(i)=200.5900d0 + end select + end do + + !-definindo menor e maior massa atomica + + massmax=0.d0 + do i=1,natom + massmax=max(massmax,mass(i)) + end do + + massmin=massmax + do i=1,natom + massmin=min(massmin,mass(i)) + end do + + return + + end subroutine atomic_mass + +end module input diff --git a/SRC/MAIN/main.f90 b/SRC/MAIN/main.f90 new file mode 100644 index 0000000..0ea145c --- /dev/null +++ b/SRC/MAIN/main.f90 @@ -0,0 +1,91 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +program HICOLM + !******************************************************************************************* + !programa principal responsavel por carregar os modulos essenciais para efetuar os cálculos* + !******************************************************************************************* + use input ! parametros de entrada + use alloc_arrays ! alocando arrays essenciais + use estrutura ! definindo espaço real + use brillouin ! definindo zona de brillouin + use molecular_dynamics ! metodo Dinâmica Molecular + use tight_binding ! metodo Tight-Binding + use outfile ! imprimindo informacoes em arquivo out + + implicit none + + real(8) :: t0,t1,t2,t3,t4 + character(10) host,time + character(8) date + + open(6,file='HICOLM.out',status='unknown') ! imprimindo arquivo out + + call cpu_time(t0) + + t1=0.d0 + t2=0.d0 + t3=0.d0 + t4=0.d0 + + !-elapsed time information + + call date_and_time(Date=date) + call date_and_time(TIME=time) + call hostnm(host) + + !-cabecalho + ! + write(6,'(5x,a55)')'HICOLM: Multi-Methods for Molecules and Condensed Systems' + write(6,*) + write(6,'(''Host: '',2x,a10)')host + write(6,'(''Date: '',2x,a8)')date + write(6,'(''Time: '',2x,a10)')time + write(6,*) + + !======================================================== + !-obtendo valores iniciais + call cte + !======================================================== + !-definindo parametros de entrada + call entrada(t1) + !======================================================== + !-alocando arrays + call system_arrays + !======================================================== + !-definindo coordenadas atomicas + call coordenadas(t2) + !======================================================== + !-definindo vetores da rede reciproca + call reciprocal + !======================================================== + !-calculando Dinâmica molecular + select case(method) + case('TB') + call tb(t3) + case('MD') + call md(t3) + end select + !======================================================== + !-calculando propriedades + !if(ebndtot.eq.1)call solving(t4) + !======================================================== + !-imprimindo informacoes em ficheiro de saida + call printfile(t0,t1,t2,t3,t4) + !======================================================== + +end program HICOLM diff --git a/SRC/MAIN/outfile.f90 b/SRC/MAIN/outfile.f90 new file mode 100644 index 0000000..eeab11a --- /dev/null +++ b/SRC/MAIN/outfile.f90 @@ -0,0 +1,71 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module outfile + + use input + use estrutura + +contains + + subroutine printfile(t0,t1,t2,t3,t4) + + implicit none + + integer i + real(8) t0,t1,t2,t3,t4,tf + + call cpu_time(tf) + + tf=tf-t0 + + write(6,*)('-',i=1,70) + write(6,'('' input = '',f8.4)') t1 + write(6,'('' coordinates = '',f8.4)') t2 + write(6,'('' m. mechanics = '',f8.4)') t3 + write(6,'('' solving = '',f8.4)') t4 + write(6,*)('-',i=1,70) + write(6,'('' Elapsed time = '',f8.2,'' seconds'')') tf + write(6,*) + write(6,'(93a1)')('#',i=1,93) + write(6,*)('FIM!',i=1,20) + write(6,'(93a1)')('#',i=1,93) + write(6,*) + + !======================================================== + !-aviso de direitos autorais + + write(6,'(5x,a46)')'Copyright (C) 2019 Flaviano Williams Fernandes' + write(6,*) + write(6,'(5x,a68)')'This program is free software: you can redistribute it and/or modify' + write(6,'(5x,a68)')'it under the terms of the GNU General Public License as published by' + write(6,'(5x,a40)')'the Free Software Foundation, version 3.' + write(6,*) + write(6,'(5x,a63)')'This program is distributed in the hope that it will be useful,' + write(6,'(5x,a62)')'but WITHOUT ANY WARRANTY; without even the implied warranty of' + write(6,'(5x,a61)')'MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the' + write(6,'(5x,a44)')'GNU General Public License for more details.' + write(6,*) + write(6,'(5x,a65)')'You should have received a copy of the GNU General Public License' + write(6,'(5x,a66)')'along with this program. If not, see .' + write(6,*) + + return + + end subroutine printfile + +end module outfile diff --git a/SRC/MAIN/sistema.f90 b/SRC/MAIN/sistema.f90 new file mode 100644 index 0000000..7fb196c --- /dev/null +++ b/SRC/MAIN/sistema.f90 @@ -0,0 +1,65 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module sistema + !******************************************************************************************** + ! modulo de dimensionamento estático de arrays * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !******************************************************************************************** + public + + integer ntpmax,natmax,nkmax,nbandmax,nparammax,nprllmmax,nkrlxmax,dkrlxmax + integer lmax,mmax,molecmax,bendmax,bondmax,torsmax + ! + !----------------------------------------------------------------- + !-nparammax: Limite de parametros SK + !- nbandmax: Limite de bandas de calculo DFT + !- nkmax: Limite de pontos K + !- natmax: Limite de atomos + !- ntpmax: Limite de tipos atomicos + !- lpmmax: Limite de subniveis magneticos + !- mmax: Limite do subnivel magnetico + !- molecmax: Limite de moleculas + !- bendmax: Limite de parametros de deformacao angular + !- bondmax: Limite de parametros de estiramento + !- torsmax: Limite de parametros de torsão + !- nkrlxmax: Limite de pontos K para ajuste dos parametros SK + !- dkrlxmax: Limite de pontos K para ajuste dos parametros SK + !---------------------------------------------------------------- + ! + parameter (natmax=2000) + parameter (ntpmax=10) + parameter (nkmax=150000) + parameter (nprllmmax=4) + parameter (nparammax=10) + + parameter (nbandmax=5000) + + parameter (lmax=4) + parameter (mmax=9) + + parameter (nkrlxmax=100) + parameter (dkrlxmax=100) + + parameter (molecmax=500) + + parameter (bendmax=20) + parameter (bondmax=30) + parameter (torsmax=10) + +end module sistema diff --git a/SRC/MAIN/utils.f90 b/SRC/MAIN/utils.f90 new file mode 100644 index 0000000..bb15be5 --- /dev/null +++ b/SRC/MAIN/utils.f90 @@ -0,0 +1,116 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module utils + !**************************************************************************************** + ! Utilitários * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !**************************************************************************************** + + use input + +contains + + double precision function heaviside(t) + !************************************************************************************ + ! Funcao de truncamento Heaviside * + !************************************************************************************ + + implicit none + + real(8) t + + heaviside=0.5d0*(1.d0+t/max(abs(t),1.d-8)) + + return + + end function heaviside + + subroutine spline_cubic(dh,func,funcl,ai,bi,ci,di) + !************************************************************************************ + ! Interpolacao cubica - spline * + !************************************************************************************ + + implicit none + + integer i,INFO + integer IPIV(3) + real(8) dh(3),func(3),funcl(3),ai(3),bi(3),ci(3),di(3) + real(8) spa(3,3),spb(3,1) + + !-montando matriz A do sistema Ax=B + + spa(1,1)=2.d0*dh(1) + spa(1,2)=dh(1) + spa(1,3)=0.d0 + + spa(2,1)=dh(1) + spa(2,2)=2.d0*(dh(1)+dh(2)) + spa(2,3)=dh(2) + + spa(3,1)=0.d0 + spa(3,2)=dh(2) + spa(3,3)=2.d0*dh(2) + + !-montando matriz B do sistema Ax=B + + spb(1,1)=3.d0*(func(2)-func(1))/dh(1)-3.d0*funcl(1) + spb(2,1)=3.d0*(func(3)-func(2))/dh(2)-3.d0*(func(2)-func(1))/dh(1) + spb(3,1)=-3.d0*(func(3)-func(2))/dh(2)+3.d0*funcl(3) + + !-fatorizando matriz principal + + call dgetrf(3,3,spa,3,IPIV,INFO) + + if(INFO.eq.0)then + call dgetrs('N',3,1,spa,3,IPIV,spb,3,INFO) + else + write(*,*)'spline_cubic: Error!!!!',INFO + stop + end if + + do i=1,3 + ci(i)=spb(i,1) + end do + + do i=1,2 + ai(i)=func(i) + bi(i)=(func(i+1)-func(i))/dh(i)-dh(i)*(2.d0*ci(i)+ci(i+1))/3.d0 + di(i)=(ci(i+1)-ci(i))/(3.d0*dh(i)) + end do + + return + + end subroutine spline_cubic + + integer function kronij(i,j) + !************************************************************************************ + ! Delta de Kronecker * + !************************************************************************************ + + implicit none + + integer i,j + + kronij=int((float(i+j)-abs(i-j))/(float(i+j)+abs(i-j))) + + return + + end function kronij + +end module utils diff --git a/SRC/MD/bends_module.f90 b/SRC/MD/bends_module.f90 new file mode 100644 index 0000000..ed99641 --- /dev/null +++ b/SRC/MD/bends_module.f90 @@ -0,0 +1,296 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module bends_module + !****************************************************************************************** + ! Contribuicao de deformacao para o campo de força: * + ! - Energia potencial; * + ! - Forças atômicas; * + ! - Virial; * + ! - Stress. * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use input + use utils + use estrutura + use alloc_arrays + + integer, allocatable :: bendij(:,:) + integer, allocatable :: bendim(:),bendib(:) + + integer nbendstp + + save bendij,bendim,bendib,nbendstp + +contains + + subroutine bends_alloc + !**************************************************************************************** + ! Alocacao de variaveis globais * + !**************************************************************************************** + + implicit none + + allocate(bendij(3,nbends)) + allocate(bendim(nbends)) + allocate(bendib(nbends)) + + return + + end subroutine bends_alloc + + subroutine bends_convert + !**************************************************************************************** + ! Conversao de unidades de medida: * + ! Unidades de entrada ---> a.u. * + !**************************************************************************************** + + implicit none + + integer i,j + + !-convertendo unidades de medida + + do i=1,nmolec + do j=1,bendscnt(i) + select case(bends(i,j)) + case(1) + parbend(i,j,1)=parbend(i,j,1)/econv + parbend(i,j,2)=parbend(i,j,2)/aconv + end select + end do + end do + + return + + end subroutine bends_convert + + subroutine bends_counts + !**************************************************************************************** + ! Contagem do número de deformacoes * + !**************************************************************************************** + + implicit none + + integer, allocatable :: chk(:,:) + + integer nx,nxx,i,j,k,ni,nj,nk,nkb,np + + !-alocando array + + nx=0 + do i=1,nmolec + nx=max(nx,bendscnt(i)) + end do + + allocate(chk(nmolec,nbends)) + + !-checando viabilidade dos bonds + + nkb=1 + + do i=1,nmolec + do j=1,bendscnt(i) + select case(bends(i,j)) + case(1) + nkb=2 + end select + chk(i,j)=1 + do k=1,nkb + if(parbend(i,j,k).eq.0.d0)chk(i,j)=0 + end do + end do + end do + + !-calculando bends intramoleculares + + np=0 + nx=1 + do i=1,nmolec + nxx=0 + do j=1,ntmolec(i) + do k=1,bendscnt(i) + ni=np+molbend(i,k,2) + nj=np+molbend(i,k,1) + nk=np+molbend(i,k,3) + if(chk(i,k).eq.1)then + bendij(1,nx)=ni + bendij(2,nx)=nj + bendij(3,nx)=nk + bendim(nx)=i + bendib(nx)=k + nxx=nxx+1 + nx=nx+1 + end if + end do + np=np+nxmolec(i) + end do + bendsmlc(i)=nxx + end do + + nbendstp=nx-1 + + !-limpando memoria + + deallocate(chk) + + return + + end subroutine bends_counts + + subroutine bends_calc(enbend,virbend) + !**************************************************************************************** + ! - Energia potencial; * + ! - Contribuicao para o virial; * + ! - Contribuicao para o stress; * + ! - Forças atômicas. * + !**************************************************************************************** + + implicit none + + integer i,ia,ib,ic,im,in + real(8) pot,fa,drij(3),drik(3),theta,dr1,dr2 + real(8) enbend,virbend + + do i=1,nbendstp + + ia=bendij(1,i) + ib=bendij(2,i) + ic=bendij(3,i) + im=bendim(i) + in=bendib(i) + + call ccpmm(ia,ib,drij(1),drij(2),drij(3)) + call ccpmm(ia,ic,drik(1),drik(2),drik(3)) + + dr1=max(1.d-4,sqrt(drij(1)**2+drij(2)**2+drij(3)**2)) + dr2=max(1.d-4,sqrt(drik(1)**2+drik(2)**2+drik(3)**2)) + + theta=max(1.d-4,acos((drij(1)*drik(1)+drij(2)*drik(2)+drij(3)*drik(3))/(dr1*dr2))) + + call bends_flags(im,in,theta,pot,fa) + call bends_force(ia,ib,ic,drij,drik,dr1,dr2,theta,fa,virbend) + + enbend=enbend+pot + + end do + + return + + end subroutine bends_calc + + subroutine bends_flags(im,in,theta,pot,fa) + !**************************************************************************************** + ! Compontente angular * + !**************************************************************************************** + + implicit none + + integer im,in + real(8) theta,fa,pot + + !-atribuindo valores iniciais + + pot=0.d0 + fa=0.d0 + + !-calculo da componente dU/dtheta + + select case(bends(im,in)) + case(1) + pot=0.5d0*parbend(im,in,1)*(theta-parbend(im,in,2))**2 + fa=parbend(im,in,1)*(theta-parbend(im,in,2)) + end select + + return + + end subroutine bends_flags + + subroutine bends_force(i1,i2,i3,drij,drik,dr1,dr2,theta,fa,virbend) + !**************************************************************************************** + ! - Contribuicao para o virial * + ! - Contribuicao para o stress * + ! - Forcas dos atomos i, j e k * + !**************************************************************************************** + + implicit none + + integer i,j,i1,i2,i3,ix(3) + real(8) drij(3),drik(3),derij(3,3),fbi(3),fbj(3),fbk(3),dr1,dr2,theta,virbend,fa + + !-calculo da componente dtheta/dr + + ix(1)=i1 + ix(2)=i2 + ix(3)=i3 + + do j=1,3 + do i=1,3 + derij(i,j)=(kronij(ix(i),ix(2))-kronij(ix(i),ix(1)))*drik(j)/(dr1*dr2) & + +(kronij(ix(i),ix(3))-kronij(ix(i),ix(1)))*drij(j)/(dr1*dr2) & + -cos(theta)*((kronij(ix(i),ix(2))-kronij(ix(i),ix(1)))*drij(j)/dr1**2 & + +(kronij(ix(i),ix(3))-kronij(ix(i),ix(1)))*drik(j)/dr2**2) + end do + end do + + !-calculo das forças atomicas i, j e k + + fbi(1)=fa*derij(1,1)/sin(theta) + fbi(2)=fa*derij(1,2)/sin(theta) + fbi(3)=fa*derij(1,3)/sin(theta) + + fbj(1)=fa*derij(2,1)/sin(theta) + fbj(2)=fa*derij(2,2)/sin(theta) + fbj(3)=fa*derij(2,3)/sin(theta) + + fbk(1)=fa*derij(3,1)/sin(theta) + fbk(2)=fa*derij(3,2)/sin(theta) + fbk(3)=fa*derij(3,3)/sin(theta) + + fax(i1)=fax(i1)+fbi(1) + fay(i1)=fay(i1)+fbi(2) + faz(i1)=faz(i1)+fbi(3) + + fax(i2)=fax(i2)+fbj(1) + fay(i2)=fay(i2)+fbj(2) + faz(i2)=faz(i2)+fbj(3) + + fax(i3)=fax(i3)+fbk(1) + fay(i3)=fay(i3)+fbk(2) + faz(i3)=faz(i3)+fbk(3) + + !-contribuicao para o virial + + virbend=virbend+(fbj(1)*drij(1)+fbj(2)*drij(2)+fbj(3)*drij(3))& + +(fbk(1)*drik(1)+fbk(2)*drik(2)+fbk(3)*drik(3)) + + !-contribuicao para o stress + + str(1)=str(1)-(fbj(1)*drij(1)+fbk(1)*drik(1)) + str(2)=str(2)-(fbj(2)*drij(2)+fbk(2)*drik(2)) + str(3)=str(3)-(fbj(3)*drij(3)+fbk(3)*drik(3)) + str(4)=str(4)-(fbj(3)*drij(2)+fbk(3)*drik(2)) + str(5)=str(5)-(fbj(1)*drij(3)+fbk(1)*drik(3)) + str(6)=str(6)-(fbj(2)*drij(1)+fbk(2)*drik(1)) + + return + + end subroutine bends_force + +end module bends_module diff --git a/SRC/MD/bonds_module.f90 b/SRC/MD/bonds_module.f90 new file mode 100644 index 0000000..5858570 --- /dev/null +++ b/SRC/MD/bonds_module.f90 @@ -0,0 +1,271 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module bonds_module + !****************************************************************************************** + ! Contribuicoes de estiramento para o campo de força: * + ! - Energia potencial; * + ! - Forças atômicas; * + ! - Virial; * + ! - Stress. * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use input + use utils + use estrutura + use alloc_arrays + + integer, allocatable :: bondij(:,:) + integer, allocatable :: bondim(:),bondib(:) + + integer nbondstp + + save bondij,bondim,bondib,nbondstp + +contains + + subroutine bonds_alloc + !**************************************************************************************** + ! Alocacao de variaveis globais * + !**************************************************************************************** + + implicit none +! + allocate(bondij(2,nbonds)) + allocate(bondim(nbonds)) + allocate(bondib(nbonds)) +! + end subroutine bonds_alloc + + subroutine bonds_convert + !**************************************************************************************** + ! Conversao de unidades de medida: * + ! Unidades de entrada ---> a.u. * + !**************************************************************************************** + + implicit none + + integer i,j + + !-convertendo unidades de medida + + do i=1,nmolec + do j=1,bondscnt(i) + select case(bonds(i,j)) + case(1) + parbnd(i,j,1)=parbnd(i,j,1)/econv + parbnd(i,j,2)=parbnd(i,j,2)/kconv + parbnd(i,j,3)=parbnd(i,j,3)/rconv + case(2) + parbnd(i,j,1)=parbnd(i,j,1)/(econv/rconv**2.d0) + parbnd(i,j,2)=parbnd(i,j,2)/rconv + end select + end do + end do + + return + + end subroutine bonds_convert + + subroutine bonds_counts + !**************************************************************************************** + ! Contagem do número de diedros * + !**************************************************************************************** + + implicit none + + integer, allocatable :: chk(:,:) + + integer nx,nxx,i,j,k,ni,nj,np,nkb + + !-alocando array + + allocate(chk(nmolec,nbonds)) + + !-checando viabilidade de bonds + + nkb=1 + + do i=1,nmolec + do j=1,bondscnt(i) + select case(bonds(i,j)) + case(1) + nkb=3 + case(2) + nkb=2 + end select + chk(i,j)=1 + do k=1,nkb + if(parbnd(i,j,k).eq.0.d0)chk(i,j)=0 + end do + end do + end do + + !-calculando bonds intramoleculares + + np=0 + nx=1 + do i=1,nmolec + nxx=0 + do j=1,ntmolec(i) + do k=1,bondscnt(i) + ni=np+molbond(i,k,1) + nj=np+molbond(i,k,2) + if(chk(i,k).eq.1)then + bondij(1,nx)=ni + bondij(2,nx)=nj + bondim(nx)=i + bondib(nx)=k + nxx=nxx+1 + nx=nx+1 + end if + end do + np=np+nxmolec(i) + end do + bondsmlc(i)=nxx + end do + + nbondstp=nx-1 + + !-limpando memoria + + deallocate(chk) + + return + + end subroutine bonds_counts + + subroutine bonds_calc(enbond,virbond) + !**************************************************************************************** + ! - Energia potencial; * + ! - Contribuicao para o virial; * + ! - Contribuicao para o stress; * + ! - Forças atômicas. * + !**************************************************************************************** + + implicit none + + integer i,ia,ib,im,in + real(8) xvz,yvz,zvz,fr,dr,pot + real(8) enbond,virbond + + do i=1,nbondstp + + ia=bondij(1,i) + ib=bondij(2,i) + im=bondim(i) + in=bondib(i) + + call ccpmm(ia,ib,xvz,yvz,zvz) + + !distancia interatomica + + dr=sqrt(xvz**2+yvz**2+zvz**2) + + call bonds_flags(im,in,dr,pot,fr) + call bonds_force(ia,ib,xvz,yvz,zvz,fr,virbond) + + enbond=enbond+pot + + end do + + return + + end subroutine bonds_calc + + subroutine bonds_flags(im,in,dr,pot,fr) + !**************************************************************************************** + ! Compontente angular * + !**************************************************************************************** + + implicit none + + integer im,in,ii + real(8) pot,fr,dr,prm(3) + + !-valores iniciais + + pot=0.d0 + fr=0.d0 + + !-calculo do gradiente e energia potencial + + select case(bonds(im,in)) + case(1) + do ii=1,3 + prm(ii)=parbnd(im,in,ii) + end do + pot=prm(1)*(exp(-2.d0*prm(2)*(dr-prm(3))) & + -2.d0*exp(-prm(2)*(dr-prm(3)))) + + fr=2.d0*prm(1)*prm(2)*(exp(-2.d0*prm(2)*(dr-prm(3))) & + -exp(-prm(2)*(dr-prm(3))))/dr + case(2) + do ii=1,2 + prm(ii)=parbnd(im,in,ii) + end do + pot=0.5d0*prm(1)*(dr-prm(2))**2 + + fr=-prm(1)*(dr-prm(2))/dr + end select + + return + + end subroutine bonds_flags + + subroutine bonds_force(i,j,xvz,yvz,zvz,fr,virbond) + !**************************************************************************************** + ! - Contribuicao para o virial * + ! - Contribuicao para o stress * + ! - Forcas dos atomos i e j * + !**************************************************************************************** + + implicit none + + integer i,j + real(8) xvz,yvz,zvz,fr,virbond + + !-contribuicao para as forcas atomicas + + fax(i)=fax(i)-fr*xvz + fay(i)=fay(i)-fr*yvz + faz(i)=faz(i)-fr*zvz + + fax(j)=fax(j)+fr*xvz + fay(j)=fay(j)+fr*yvz + faz(j)=faz(j)+fr*zvz + + !-contribuicao para o virial + + virbond=virbond+fr*(xvz**2+yvz**2+zvz**2) + + !-contribuição para o stress + + str(1)=str(1)-(fr*xvz)*xvz + str(2)=str(2)-(fr*yvz)*yvz + str(3)=str(3)-(fr*zvz)*zvz + str(4)=str(4)-(fr*zvz)*yvz + str(5)=str(5)-(fr*xvz)*zvz + str(6)=str(6)-(fr*yvz)*xvz + + return + + end subroutine bonds_force + +end module bonds_module diff --git a/SRC/MD/coulomb_module.f90 b/SRC/MD/coulomb_module.f90 new file mode 100644 index 0000000..39884fc --- /dev/null +++ b/SRC/MD/coulomb_module.f90 @@ -0,0 +1,169 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module coulomb_module + !****************************************************************************************** + ! Contribuicao eletrostatica para o campo de força: * + ! - Energia potencial; * + ! - Forças atômicas; * + ! - Virial; * + ! - Stress. * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use input + use utils + use estrutura + use alloc_arrays + use neighbour_list + +contains + + subroutine coulomb_convert + !**************************************************************************************** + ! Conversao de unidades de medida: * + ! Unidades de entrada ---> a.u. * + !**************************************************************************************** + + implicit none + + integer i + + !-convertendo Van der Waals + + do i=1,ntpmax + parcoul(i,1)=parcoul(i,1)/elconv + end do + + return + + end subroutine coulomb_convert + + subroutine coulomb_calc(encoul,vircoul,ni,nj,xvz,yvz,zvz) + !**************************************************************************************** + ! - Energia potencial; * + ! - Contribuicao para o virial; * + ! - Contribuicao para o stress; * + ! - Forças atômicas. * + !**************************************************************************************** + + implicit none + + integer ni,nj + real(8) xvz,yvz,zvz,fr,pot + real(8) encoul,vircoul + + call coulomb_flags(atp(ni),atp(nj),xvz,yvz,zvz,pot,fr) + call coulomb_force(ni,nj,xvz,yvz,zvz,fr) + + vircoul=vircoul+fr*(xvz**2+yvz**2+zvz**2) + encoul=encoul+pot + + return + + end subroutine coulomb_calc + + subroutine coulomb_flags(i,j,xvz,yvz,zvz,pot,fr) + !**************************************************************************************** + ! Compontente angular * + !**************************************************************************************** + + implicit none + + integer i,j + real(8) pot,fr,xvz,yvz,zvz,dr,prm(2),alcoul,xij,lambda + + !-atribuindo valores iniciais + + pot=0.d0 + fr=0.d0 + + !-calculo do gradiente e potencial + + dr=sqrt(xvz**2+yvz**2+zvz**2) + + prm(1)=parcoul(i,1) + prm(2)=parcoul(j,1) + ! + select case(coulop) + case('coul') + + alcoul=1.d-1/kconv + + pot=prm(1)*prm(2)*(erfc(alcoul*dr)/dr-erfc(alcoul*rcutoff)/rcutoff & + +(erfc(alcoul*rcutoff)/rcutoff**2+(2.d0*alcoul) & + *exp(-(alcoul*rcutoff)**2)/(sqrt(pi)*rcutoff))*(dr-rcutoff)) + + fr=-prm(1)*prm(2)*(erfc(alcoul*dr)/dr**2+(2.d0*alcoul) & + *exp(-(alcoul*dr)**2)/(sqrt(pi)*dr) & + -(erfc(alcoul*rcutoff)/rcutoff**2 & + +(2.d0*alcoul)*exp(-(alcoul*rcutoff)**2)/(sqrt(pi)*rcutoff))) + + fr=-fr/dr ! -(1/r)*dU/dr + + case('escl') + + lambda=lambdafi + + xij=sqrt(2.d0*(1.d0-lambda)**2+dr**2) + + pot=prm(1)*prm(2)*lambda*(1.d0/xij+xij/rcutoff**2-2.d0/rcutoff) + + fr=prm(1)*prm(2)*lambda*(1.d0/xij**2-1.d0/rcutoff**2)/xij + + end select +! + return +! + end subroutine coulomb_flags + + subroutine coulomb_force(i,j,xvz,yvz,zvz,fr) + !**************************************************************************************** + ! - Contribuicao para o virial * + ! - Contribuicao para o stress * + ! - Forcas dos atomos i, j, k e n * + !**************************************************************************************** + + implicit none + + integer i,j + real(8) xvz,yvz,zvz,fr + + !-calculo da contribuicao da forca atomica + + fax(i)=fax(i)-fr*xvz + fay(i)=fay(i)-fr*yvz + faz(i)=faz(i)-fr*zvz + fax(j)=fax(j)+fr*xvz + fay(j)=fay(j)+fr*yvz + faz(j)=faz(j)+fr*zvz + + !-calculo da contribuição do stress + + str(1)=str(1)+(fr*xvz)*xvz + str(2)=str(2)+(fr*yvz)*yvz + str(3)=str(3)+(fr*zvz)*zvz + str(4)=str(4)+(fr*zvz)*yvz + str(5)=str(5)+(fr*xvz)*zvz + str(6)=str(6)+(fr*yvz)*xvz + + return + + end subroutine coulomb_force + +end module coulomb_module diff --git a/SRC/MD/dihedral_module.f90 b/SRC/MD/dihedral_module.f90 new file mode 100644 index 0000000..497505d --- /dev/null +++ b/SRC/MD/dihedral_module.f90 @@ -0,0 +1,381 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module dihedral_module + !****************************************************************************************** + ! Contribuicao de diedros para o campo de força: * + ! - Energia potencial; * + ! - Forças atômicas; * + ! - Virial; * + ! - Stress. * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use input + use utils + use estrutura + use alloc_arrays + + integer, allocatable :: torsijkn(:,:) + integer, allocatable :: torsim(:),torsib(:) + + integer ntorsstp + + save torsim,torsib,torsijkn,ntorsstp + +contains + + subroutine tors_alloc + !**************************************************************************************** + ! Alocacao de variaveis globais * + !**************************************************************************************** + + implicit none + + allocate(torsijkn(4,ntors)) + allocate(torsim(ntors)) + allocate(torsib(ntors)) + + return + + end subroutine tors_alloc + + subroutine tors_convert + !**************************************************************************************** + ! Conversao de unidades de medida: * + ! Unidades de entrada ---> a.u. * + !**************************************************************************************** + + implicit none + + integer i,j + + !-convertendo unidades de medida + + do i=1,nmolec + do j=1,torscnt(i) + select case(tors(i,j)) + case(1) + partors(i,j,1)=partors(i,j,1)/econv + partors(i,j,2)=partors(i,j,2)/aconv + end select + end do + end do + + return + + end subroutine tors_convert + + subroutine tors_counts + !**************************************************************************************** + ! Contagem do número de diedros * + !**************************************************************************************** + + implicit none + + integer, allocatable :: chk(:,:) + + integer i,j,k,nkb,nx,nxx,ni,nj,nk,nn,np + + !-alocando array + + allocate(chk(nmolec,ntors)) + + !-checando viabilidade de bonds + + nkb=1 + + do i=1,nmolec + do j=1,torscnt(i) + select case(tors(i,j)) + case(1) + nkb=1 + end select + chk(i,j)=1 + do k=1,nkb + if(partors(i,j,k).eq.0.d0)chk(i,j)=0 + end do + end do + end do + + !-calculando torsoes intramoleculares + + np=0 + nx=1 + do i=1,nmolec + nxx=0 + do j=1,ntmolec(i) + do k=1,torscnt(i) + ni=np+moltors(i,k,1) + nj=np+moltors(i,k,2) + nk=np+moltors(i,k,3) + nn=np+moltors(i,k,4) + if(chk(i,k).eq.1)then + torsijkn(1,nx)=ni + torsijkn(2,nx)=nj + torsijkn(3,nx)=nk + torsijkn(4,nx)=nn + torsim(nx)=i + torsib(nx)=k + nxx=nxx+1 + nx=nx+1 + end if + end do + np=np+nxmolec(i) + end do + torsmlc(i)=nxx + end do + + ntorsstp=nx-1 + + !-limpando memoria + + deallocate(chk) + + return + + end subroutine tors_counts + + subroutine tors_calc(entors,virtors) + !**************************************************************************************** + ! - Energia potencial; * + ! - Contribuicao para o virial; * + ! - Contribuicao para o stress; * + ! - Forças atômicas. * + !**************************************************************************************** + + implicit none + + integer i,ia,ib,ic,id,im,in + real(8) pot,fd,drij(3),drjk(3),drkn(3),vc1x,vc1y,vc1z,vc2x,vc2y,vc2z,dvc1,dvc2,phi + real(8) entors,virtors + + do i=1,ntorsstp + + ia=torsijkn(1,i) + ib=torsijkn(2,i) + ic=torsijkn(3,i) + id=torsijkn(4,i) + im=torsim(i) + in=torsib(i) + + call ccpmm(ia,ib,drij(1),drij(2),drij(3)) + call ccpmm(ib,ic,drjk(1),drjk(2),drjk(3)) + call ccpmm(ic,id,drkn(1),drkn(2),drkn(3)) + + !-produto vetorial + + vc1x=drij(2)*drjk(3)-drij(3)*drjk(2) + vc1y=drij(3)*drjk(1)-drij(1)*drjk(3) + vc1z=drij(1)*drjk(2)-drij(2)*drjk(1) + + vc2x=drjk(2)*drkn(3)-drjk(3)*drkn(2) + vc2y=drjk(3)*drkn(1)-drjk(1)*drkn(3) + vc2z=drjk(1)*drkn(2)-drjk(2)*drkn(1) + + dvc1=sqrt(vc1x**2+vc1y**2+vc1z**2) + dvc2=sqrt(vc2x**2+vc2y**2+vc2z**2) + + !-angulo do diedro + + phi=acos((vc1x*vc2x+vc1y*vc2y+vc1z*vc2z)/(dvc1*dvc2)) + + phi=max(1.d-4,phi) + + call tors_flags(im,in,phi,pot,fd) + call tors_force(ia,ib,ic,id,drij,drjk,drkn,dvc1,dvc2,phi,fd,virtors) + + entors=entors+pot + + end do + + return + + end subroutine tors_calc + + subroutine tors_flags(im,in,phi,pot,fd) + !**************************************************************************************** + ! Compontente angular * + !**************************************************************************************** + + implicit none + + integer im,in + real(8) phi,fd,pot + + !-valores iniciais + + pot=0.d0 + fd=0.d0 + + !-componente dU/dphi + + select case(tors(im,in)) + case(1) + pot=0.5d0*partors(im,in,1)*(phi-partors(im,in,2))**2 + fd=partors(im,in,1)*(phi-partors(im,in,2)) + end select + + return + + end subroutine tors_flags + + subroutine tors_force(i1,i2,i3,i4,drij,drjk,drkn,dvc1,dvc2,phi,fd,virtors) + !**************************************************************************************** + ! - Contribuicao para o virial * + ! - Contribuicao para o stress * + ! - Forcas dos atomos i, j, k e n * + !**************************************************************************************** + + implicit none + + integer i,j,ix(4),i1,i2,i3,i4 + real(8) drij(3),drjk(3),drkn(3),dvc(4,3),fbi(3),fbj(3),fbk(3),fbn(3) + real(8) dvc1,dvc2,phi,fd,virtors + + !-componente d[(rij x rjk)*(rjk x rkn)/|rij x rjk||rjk x rkn|] + + ix(1)=i1 + ix(2)=i2 + ix(3)=i3 + ix(4)=i4 + ! + do i=1,4 + do j=1,3 + dvc(i,j)=dfunc1(i1,i2,i3,i4,drij,drjk,drkn,ix(i),j)/(dvc1*dvc2) & + -0.5d0*cos(phi)*(dfunc2(i1,i2,i3,drij,drjk,ix(i),j)/dvc1**2 & + +dfunc2(i2,i3,i4,drjk,drkn,ix(i),j)/dvc2**2) + end do + end do + + !-contribuicao para as forças atomicas + + fbi(1)=fd*dvc(1,1)/sin(phi) + fbi(2)=fd*dvc(1,2)/sin(phi) + fbi(3)=fd*dvc(1,3)/sin(phi) + + fbj(1)=fd*dvc(2,1)/sin(phi) + fbj(2)=fd*dvc(2,2)/sin(phi) + fbj(3)=fd*dvc(2,3)/sin(phi) + + fbk(1)=fd*dvc(3,1)/sin(phi) + fbk(2)=fd*dvc(3,2)/sin(phi) + fbk(3)=fd*dvc(3,3)/sin(phi) + + fbn(1)=fd*dvc(4,1)/sin(phi) + fbn(2)=fd*dvc(4,2)/sin(phi) + fbn(3)=fd*dvc(4,3)/sin(phi) + + fax(i1)=fax(i1)+fbi(1) + fay(i1)=fay(i1)+fbi(2) + faz(i1)=faz(i1)+fbi(3) + + fax(i2)=fax(i2)+fbj(1) + fay(i2)=fay(i2)+fbj(2) + faz(i2)=faz(i2)+fbj(3) + + fax(i3)=fax(i3)+fbk(1) + fay(i3)=fay(i3)+fbk(2) + faz(i3)=faz(i3)+fbk(3) + + fax(i4)=fax(i4)+fbn(1) + fay(i4)=fay(i4)+fbn(2) + faz(i4)=faz(i4)+fbn(3) + + !-contribuicao para o virial + + virtors=0.d0 + + !-calculo da contribuicao para o stress + + str(1)=str(1)-(fbi(1)*drij(1)+fbj(1)*drjk(1)+fbk(1)*drkn(1)) + str(2)=str(2)-(fbi(2)*drij(2)+fbj(2)*drjk(2)+fbk(2)*drkn(2)) + str(3)=str(3)-(fbi(3)*drij(3)+fbj(3)*drjk(3)+fbk(3)*drkn(3)) + str(4)=str(4)-(fbi(3)*drij(2)+fbj(3)*drjk(2)+fbk(3)*drkn(2)) + str(5)=str(5)-(fbi(1)*drij(3)+fbj(1)*drjk(3)+fbk(1)*drkn(3)) + str(6)=str(6)-(fbi(2)*drij(1)+fbj(2)*drjk(1)+fbk(2)*drkn(1)) + + return + + end subroutine tors_force + + double precision function dfunc1(i1,i2,i3,i4,drij,drjk,drkn,i,j) + !**************************************************************************************** + ! d[(rij x rjk)*(rjk x rkn)] * + !**************************************************************************************** + + implicit none + + integer i,j,i1,i2,i3,i4 + real(8) drij(3),drjk(3),drkn(3) + + dfunc1=drij(j)*acomt(drjk,drjk,j)*(kronij(i,i3)-kronij(i,i4)) & + +drij(j)*acomt(drjk,drkn,j)*(kronij(i,i3)-kronij(i,i2)) & + +drjk(j)*acomt(drij,drjk,j)*(kronij(i,i4)-kronij(i,i3)) & + +drjk(j)*acomt(drjk,drkn,j)*(kronij(i,i2)-kronij(i,i1)) & + +drkn(j)*acomt(drij,drjk,j)*(kronij(i,i3)-kronij(i,i2)) & + +drkn(j)*acomt(drjk,drjk,j)*(kronij(i,i1)-kronij(i,i2)) & + +2.d0*drjk(j)*acomt(drij,drkn,j)*(kronij(i,i2)-kronij(i,i3)) + + return + + end function dfunc1 + + double precision function dfunc2(i1,i2,i3,dri1,dri2,i,j) + !**************************************************************************************** + ! d[(rjk x rkn)**2] * + !**************************************************************************************** + + implicit none + + integer i,j,i1,i2,i3 + real(8) dri1(3),dri2(3) + + dfunc2=dri1(j)*acomt(dri2,dri2,j)*(kronij(i,i2)-kronij(i,i1)) & + +dri1(j)*acomt(dri1,dri2,j)*(kronij(i,i2)-kronij(i,i3)) & + +dri2(j)*acomt(dri1,dri1,j)*(kronij(i,i3)-kronij(i,i2)) & + +dri2(j)*acomt(dri1,dri2,j)*(kronij(i,i1)-kronij(i,i2)) + + dfunc2=2.d0*dfunc2 + + return + + end function dfunc2 + + double precision function acomt(x1,x2,k) + !**************************************************************************************** + ! Anticomutador * + !**************************************************************************************** + + implicit none + + integer i,k + real(8) sum,x1(3),x2(3) + + sum=0.d0 + do i=1,3 + sum=sum+(1.d0-kronij(i,k))*x1(i)*x2(i) + end do + + acomt=sum + + return + + end function acomt + +end module dihedral_module diff --git a/SRC/MD/ensemble_npt.f90 b/SRC/MD/ensemble_npt.f90 new file mode 100644 index 0000000..0977374 --- /dev/null +++ b/SRC/MD/ensemble_npt.f90 @@ -0,0 +1,148 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module ensemble_npt + !**************************************************************************************** + ! Integradores de movimento do ensemble NPT * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !**************************************************************************************** + + use input + use estrutura + use force_field + +contains + + subroutine npt_ber_vv(temp,press,ekinet,encoul,enbond,enbend,entors,envdw,entrsff,virvdw, & + virbond,virbend,virtors,vircoul,virtrsff) + !************************************************************************************* + ! Controle da temperatura e pressão pelo algoritmo Berendsen * + !************************************************************************************* + + implicit none + + integer i,j + real(8) temp,press,xhi,eta,ekinet,sigma + real(8) virvdw,virbond,virbend,virtors,vircoul,virtrsff,virtot + real(8) encoul,enbond,enbend,entors,envdw,entrsff + + !-preparando parametro de escalonamento isotrópico + + eta=(1.d0-bfactor*dtime*(preext-press)/pstat)**(1.d0/3.d0) + + !-calculando posições no instante t+dt posterior + + do i=1,natom + vax(i)=vax(i)+fax(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vay(i)=vay(i)+fay(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vaz(i)=vaz(i)+faz(i)*(0.5d0*dtime)*fztp(i)/mass(i) + xa(i)=xa(i)*eta+vax(i)*dtime + ya(i)=ya(i)*eta+vay(i)*dtime + za(i)=za(i)*eta+vaz(i)*dtime + end do + + !-redefinindo volume e vetores de rede + + do i=1,3 + do j=1,3 + v(i,j)=v(i,j)*eta + end do + end do + + volume=volume*eta**3 + + a=sqrt(v(1,1)**2+v(1,2)**2+v(1,3)**2) + b=sqrt(v(2,1)**2+v(2,2)**2+v(2,3)**2) + c=sqrt(v(3,1)**2+v(3,2)**2+v(3,3)**2) + + !-checando dimensoes da caixa + + if((rcutoff+drcutoff).gt.0.5d0*a)stop 'npt_ber_vv: rcutoff exceeds the half-box size' + if((rcutoff+drcutoff).gt.0.5d0*b)stop 'npt_ber_vv: rcutoff exceeds the half-box size' + if((rcutoff+drcutoff).gt.0.5d0*c)stop 'npt_ber_vv: rcutoff exceeds the half-box size' + + !-aplicando condicoes de contorno inversa + + call ccp_inv + + !-calculo das forças no instante t+dt posterior + + call ff_modules(encoul,enbond,enbend,entors,envdw,entrsff,virvdw,virbond, & + virbend,virtors,vircoul,virtrsff) + + !-calculando velocidades no instante t+dt posterior + + do i=1,natom + vax(i)=vax(i)+fax(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vay(i)=vay(i)+fay(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vaz(i)=vaz(i)+faz(i)*(0.5d0*dtime)*fztp(i)/mass(i) + end do + + !-calculo da energia cinetica total + + ekinet=0.d0 + do i=1,natom + ekinet=ekinet+mass(i)*(vax(i)**2+vay(i)**2+vaz(i)**2) + end do + + ekinet=0.5d0*ekinet + + !-preparando parametro de escalonamento + + sigma=0.5d0*nfree*text + + xhi=sqrt(1.d0+dtime*(sigma/ekinet-1.d0)/tstat) + + !-rescalonando velocidades + + do i=1,natom + vax(i)=vax(i)*xhi + vay(i)=vay(i)*xhi + vaz(i)=vaz(i)*xhi + end do + + !-calculo da temperatura + + temp=2.d0*ekinet/nfree + + !-calculo da pressao + + virtot=virvdw+virbond+virbend+virtors+vircoul+virtrsff + + press=(2.d0*ekinet+3.d0*temp+virtot+virvdw_corr)/(3.d0*volume) + + !-calculo do stress + + do i=1,natom + str(1)=str(1)-mass(i)*vax(i)*vax(i) + str(2)=str(2)-mass(i)*vay(i)*vay(i) + str(3)=str(3)-mass(i)*vaz(i)*vaz(i) + str(4)=str(4)-mass(i)*vaz(i)*vay(i) + str(5)=str(5)-mass(i)*vax(i)*vaz(i) + str(6)=str(6)-mass(i)*vay(i)*vax(i) + end do + + do i=1,6 + str(i)=str(i)/volume + end do + + return + + end subroutine npt_ber_vv + +end module ensemble_npt diff --git a/SRC/MD/ensemble_nve.f90 b/SRC/MD/ensemble_nve.f90 new file mode 100644 index 0000000..b362c95 --- /dev/null +++ b/SRC/MD/ensemble_nve.f90 @@ -0,0 +1,110 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module ensemble_nve + !**************************************************************************************** + ! Integradores de movimento do ensemble NPT * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !**************************************************************************************** + + use input + use estrutura + use force_field + +contains + + subroutine nve_vv(temp,press,ekinet,encoul,enbond,enbend,entors,envdw,entrsff,virvdw, & + virbond,virbend,virtors,vircoul,virtrsff) + !************************************************************************************* + ! Ensemble microcanonico * + !************************************************************************************* + + implicit none + + integer i + real(8) temp,press,ekinet + real(8) virvdw,virbond,virbend,virtors,vircoul,virtrsff,virtot + real(8) encoul,enbond,enbend,entors,envdw,entrsff + + !-calculando posições no instante t+dt posterior + + do i=1,natom + vax(i)=vax(i)+fax(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vay(i)=vay(i)+fay(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vaz(i)=vaz(i)+faz(i)*(0.5d0*dtime)*fztp(i)/mass(i) + xa(i)=xa(i)+vax(i)*dtime + ya(i)=ya(i)+vay(i)*dtime + za(i)=za(i)+vaz(i)*dtime + end do + + !-aplicando condicoes de contorno inversa + + call ccp_inv + + !-calculo das forças no instante t+dt posterior + + call ff_modules(encoul,enbond,enbend,entors,envdw,entrsff,virvdw,virbond,virbend,virtors, & + vircoul,virtrsff) + + !-calculando velocidades no instante t+dt posterior + + do i=1,natom + vax(i)=vax(i)+fax(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vay(i)=vay(i)+fay(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vaz(i)=vaz(i)+faz(i)*(0.5d0*dtime)*fztp(i)/mass(i) + end do + + !-calculo da energia cinetica total + + ekinet=0.d0 + do i=1,natom + ekinet=ekinet+mass(i)*(vax(i)**2+vay(i)**2+vaz(i)**2) + end do + + ekinet=0.5d0*ekinet + + !-calculo da temperatura + + temp=2.d0*ekinet/nfree + + !-calculo da pressao + + virtot=virvdw+virbond+virbend+virtors+vircoul+virtrsff + + press=(2.d0*ekinet+3.d0*temp+virtot+virvdw_corr)/(3.d0*volume) + + !-calculo do stress + + do i=1,natom + str(1)=str(1)-mass(i)*vax(i)*vax(i) + str(2)=str(2)-mass(i)*vay(i)*vay(i) + str(3)=str(3)-mass(i)*vaz(i)*vaz(i) + str(4)=str(4)-mass(i)*vaz(i)*vay(i) + str(5)=str(5)-mass(i)*vax(i)*vaz(i) + str(6)=str(6)-mass(i)*vay(i)*vax(i) + end do + + do i=1,6 + str(i)=str(i)/volume + end do + + return + + end subroutine nve_vv + +end module ensemble_nve diff --git a/SRC/MD/ensemble_nvt.f90 b/SRC/MD/ensemble_nvt.f90 new file mode 100644 index 0000000..f661192 --- /dev/null +++ b/SRC/MD/ensemble_nvt.f90 @@ -0,0 +1,124 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module ensemble_nvt + !**************************************************************************************** + ! Integradores de movimento do ensemble NVT * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !**************************************************************************************** + + use input + use estrutura + use force_field + +contains + + subroutine nvt_ber_vv(temp,press,ekinet,encoul,enbond,enbend,entors,envdw,entrsff,virvdw, & + virbond,virbend,virtors,vircoul,virtrsff) + !************************************************************************************* + ! Controle da temperatura pelo algoritmo Berendsen * + !************************************************************************************* + + implicit none + + integer i + real(8) temp,press,xhi,ekinet,sigma + real(8) virvdw,virbond,virbend,virtors,vircoul,virtrsff,virtot + real(8) encoul,enbond,enbend,entors,envdw,entrsff + + !-calculando posições no instante t+dt posterior + + do i=1,natom + vax(i)=vax(i)+fax(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vay(i)=vay(i)+fay(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vaz(i)=vaz(i)+faz(i)*(0.5d0*dtime)*fztp(i)/mass(i) + xa(i)=xa(i)+vax(i)*dtime + ya(i)=ya(i)+vay(i)*dtime + za(i)=za(i)+vaz(i)*dtime + end do + + !-aplicando condicoes de contorno + + call ccp_inv + + !-calculo das forças no instante t+dt posterior + + call ff_modules(encoul,enbond,enbend,entors,envdw,entrsff,virvdw,virbond,virbend,virtors, & + vircoul,virtrsff) + + !-calculando velocidades no instante t+dt posterior + + do i=1,natom + vax(i)=vax(i)+fax(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vay(i)=vay(i)+fay(i)*(0.5d0*dtime)*fztp(i)/mass(i) + vaz(i)=vaz(i)+faz(i)*(0.5d0*dtime)*fztp(i)/mass(i) + end do + + !-calculo da energia cinetica + + ekinet=0.d0 + do i=1,natom + ekinet=ekinet+mass(i)*(vax(i)**2+vay(i)**2+vaz(i)**2) + end do + + ekinet=0.5d0*ekinet + + !-preparando parametro de escalonamento da temperatura + + sigma=0.5d0*nfree*text + + xhi=sqrt(1.d0+dtime*(sigma/ekinet-1.d0)/tstat) + + !-rescalonando velocidades + + do i=1,natom + vax(i)=vax(i)*xhi + vay(i)=vay(i)*xhi + vaz(i)=vaz(i)*xhi + end do + + !-recalculando temperatura + + temp=2.d0*ekinet/nfree + + !-calculo da pressao + + virtot=virvdw+virbond+virbend+virtors+vircoul+virtrsff + + press=(2.d0*ekinet+3.d0*temp+virtot+virvdw_corr)/(3.d0*volume) + + !-calculo do stress + + do i=1,natom + str(1)=str(1)-mass(i)*vax(i)*vax(i) + str(2)=str(2)-mass(i)*vay(i)*vay(i) + str(3)=str(3)-mass(i)*vaz(i)*vaz(i) + str(4)=str(4)-mass(i)*vaz(i)*vay(i) + str(5)=str(5)-mass(i)*vax(i)*vaz(i) + str(6)=str(6)-mass(i)*vay(i)*vax(i) + end do + + do i=1,6 + str(i)=str(i)/volume + end do + + return + + end subroutine nvt_ber_vv + +end module ensemble_nvt diff --git a/SRC/MD/force_field.f90 b/SRC/MD/force_field.f90 new file mode 100644 index 0000000..b9c9ba1 --- /dev/null +++ b/SRC/MD/force_field.f90 @@ -0,0 +1,244 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module force_field + !****************************************************************************************** + ! Contribuicao de diedros para o campo de força: * + ! - Energia potencial; * + ! - Forças atômicas; * + ! - Virial; * + ! - Stress. * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use input + use alloc_arrays + use bonds_module + use bends_module + use dihedral_module + use vdw_module + use coulomb_module + use tersoff_module + +contains + + subroutine ff_prepare + !*************************************************************************************** + ! Preparando campo de forca * + !*************************************************************************************** + + implicit none + + integer i + + write(6,'(96a1)')('#',i=1,71) + write(6,*)'$$$$ ',('FORCE FIELD ',i=1,5),' $$$$' + write(6,'(96a1)')('#',i=1,71) + write(6,*) + + !-valores iniciais + + nbondstp=0 + nbendstp=0 + ntorsstp=0 + + do i=1,nmolec + bondsmlc(i)=0 + bendsmlc(i)=0 + torsmlc(i)=0 + end do + + !-alocando arrays (lista de vizinhos de Verlet) + + call neighbour_prepare + + !-unidades de Van der Waals + + if(nvdw.ne.0)call vdw_convert + + !-unidades de Coulomb + + if(ncoul.ne.0)call coulomb_convert + + !-unidades de estiramento + + if(nbonds.ne.0)then + call bonds_alloc + call bonds_convert + call bonds_counts + end if + + !-unidades de deformação angular + + if(nbends.ne.0)then + call bends_alloc + call bends_convert + call bends_counts + end if + + !-unidades de torção + + if(ntors.ne.0)then + call tors_alloc + call tors_convert + call tors_counts + end if + + !-unidades de Tersoff + + if(ntrsff.ne.0)call tersoff_convert + + if(nmolec.ne.0)then + write(6,*)'Molecules' + write(6,'(111a1)')('-',i=1,52) + write(6,10)'Tipo','Qde','Sites','bonds','bends','dihdl' + write(6,'(111a1)')('-',i=1,52) + do i=1,nmolec + write(6,20)namemol(i),ntmolec(i),nxmolec(i),bondsmlc(i),bendsmlc(i),torsmlc(i) + end do + write(6,'(111a1)')('-',i=1,52) + write(6,20)'Total:',moltot,natom,nbondstp,nbendstp,ntorsstp + write(6,*) + end if + + write(6,*) + write(6,30)'Total of species:',spctot,'->',(atnp(i),i=1,spctot) + write(6,*) + + !-limpando memoria + + deallocate(bondsmlc,bendsmlc,torsmlc) + + return + +10 format(a4,7x,a3,4x,a6,4x,a5,4x,a5,4x,a5) +20 format(a6,2x,i5,4(4x,i5)) +30 format(a18,i3,2x,a2,10i4) + + end subroutine ff_prepare + + subroutine ff_modules(encoul,& + enbond,enbend,entors,envdw,entrsff,virvdw,virbond,virbend,virtors,vircoul,virtrsff) + !*************************************************************************************** + ! Modulos do campo de forca (intramolecular): * + ! - Estiramento; * + ! - Deformacao; * + ! - Torsao; * + ! - Tersoff; * + ! - Van der Waals; * + ! - Eletrostatico. * + !*************************************************************************************** + + implicit none + + integer i + real(8) encoul,enbond,enbend,entors,envdw,entrsff + real(8) virvdw,virbond,virbend,virtors,vircoul,virtrsff + + !-valores iniciais + + !-energia + + encoul=0.d0 !coulombiano + enbond=0.d0 !estiramento + enbend=0.d0 !deformacao + entors=0.d0 !torção + envdw=0.d0 !Van der waals + entrsff=0.d0 !Tersoff + + !-virial + + virvdw=0.d0 !Van der Waals + virbond=0.d0 !estiramento + virbend=0.d0 !deformacao + virtors=0.d0 !torção + vircoul=0.d0 !coulombiano + virtrsff=0.d0 !Tersoff + + !-forcas atomicas + + do i=1,natom + fax(i)=0.d0 + fay(i)=0.d0 + faz(i)=0.d0 + end do + + !-stress + + do i=1,6 + str(i)=0.d0 + end do + + !-calculo da contribuicao de estiramento + + if(nbonds.ne.0)call bonds_calc(enbond,virbond) + + !-calculo da contribuicao de deformacao angular + + if(nbends.ne.0)call bends_calc(enbend,virbend) + + !-calculo da contribuicao de deformacao angular + + if(ntors.ne.0)call tors_calc(entors,virtors) + + !-calculo da contribuicao de tersoff + + if(ntrsff.ne.0)call tersoff_calc(entrsff,virtrsff) + + !-calculo das contribuicoes intermoleculares (Van der Waals e coulombiano) + + if(nvdw.ne.0.or.ncoul.ne.0)call ff_modules_inter(envdw,encoul,virvdw,vircoul) + + return + + end subroutine ff_modules + + subroutine ff_modules_inter(envdw,encoul,virvdw,vircoul) + !*************************************************************************************** + ! Modulos do campo de forca: * + ! - Van der Waals; * + ! - Eletrostatico. * + !*************************************************************************************** + + implicit none + + integer i,j,ni,nj + real(8) xvz,yvz,zvz + real(8) envdw,encoul,virvdw,vircoul + + do i=1,natom-1 + do j=1,nlist(i) + ni=i + nj=ilist(i,j) + call mic(ni,nj,xvz,yvz,zvz) + if(nvdw.ne.0)then + if(parvdw(atp(ni),atp(nj),1).ne.0.d0) & + call vdw_calc(envdw,virvdw,ni,nj,xvz,yvz,zvz) + end if + if(ncoul.ne.0)then + if(parcoul(atp(ni),1)*parcoul(atp(nj),1).ne.0.d0) & + call coulomb_calc(encoul,vircoul,ni,nj,xvz,yvz,zvz) + end if + end do + end do + + return + + end subroutine ff_modules_inter + +end module force_field diff --git a/SRC/MD/molecular_dynamics.f90 b/SRC/MD/molecular_dynamics.f90 new file mode 100644 index 0000000..bd35a84 --- /dev/null +++ b/SRC/MD/molecular_dynamics.f90 @@ -0,0 +1,289 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module molecular_dynamics + !**************************************************************************************** + ! Dinâmica Molecular * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !**************************************************************************************** + + use input + use estrutura + use force_field + use ensemble_nve + use ensemble_nvt + use ensemble_npt + use neighbour_list + + real(8) mtot + + save mtot + +contains + + subroutine md(t3) + !*************************************************************************************** + ! Obtencao das variaveis canônicas a cada intervalo de tempo * + !*************************************************************************************** + + implicit none + + integer i,ihist + real(8) t0,t3,time,temp,press + real(8) enpot,ekinet + + !-contagem do tempo absoluto + + call cpu_time(t0) + + !-preparando Dinâmica molecular + + call md_prepare + + !-imprimindo parametros de entrada + + call md_print + + !-correcao da energia VdW de curto alcance + + if(nvdw.ne.0)call vdw_corr + + !-calculo da temperatura e energia cinetica no instante inicial + + ekinet=0.d0 + do i=1,natom + ekinet=ekinet+mass(i)*(vax(i)**2+vay(i)**2+vaz(i)**2) + end do + + ekinet=0.5d0*ekinet + + write(6,'(96a1)')('#',i=1,96) + write(6,*) + write(6,'(a27,f12.4)')' Correction of VdW energy:',envdw_corr*econv + write(6,'(a27,f12.4)')'Correction of VdW pressure:',virvdw_corr*econv + write(6,*) + + !-ciclo MD + + write(6,*) + + write(6,'(111a1)')('-',i=1,88) + write(6,10)'##','Step','Time','VOLUME','TEMPERA','PRESSURE','E(TOTL)' + write(6,'(111a1)')('-',i=1,88) + + !-relaxação do sistema + + time=dtime + do i=1,nrelax + call mdloop(i,temp,press,ekinet,enpot) + write(6,20)'MD',i,time*tconv,volume*rconv**3,& + temp*teconv,press*pconv,(ekinet+enpot+envdw_corr)*econv + time=time+dtime + end do + + !-sistema em equilibrio termodinâmico + + ihist=1 + do i=nrelax+1,ntrialmax + call mdloop(i,temp,press,ekinet,enpot) + write(6,20)'MD',i,time*tconv,volume*rconv**3,& + temp*teconv,press*pconv,(ekinet+enpot+envdw_corr)*econv + if(mod(i,nhist).eq.0)call history(ihist) + time=time+dtime + end do + + write(6,'(111a1)')('-',i=1,88) + write(6,*) + + !-contagem do tempo absoluto + + call cpu_time(t3) + + t3=t3-t0 + + return + +10 format(1x,a2,6x,a4,6x,a5,9x,a6,6x,a8,7x,a8,6x,a7) +20 format(1x,a2,2x,i8,2x,e12.4,2x,e12.4,3(2x,e12.4)) + + end subroutine md + + subroutine md_prepare() + !*************************************************************************************** + ! Preparacao da dinâmica molecular: * + ! - Preparando campo de forca; * + ! - Preparando lista de vizinhos de Verlet; * + !*************************************************************************************** + + implicit none + + integer i,nwr + real(8) virvdw,virbond,virbend,virtors,vircoul,virtrsff + real(8) encoul,enbond,enbend,entors,envdw,entrsff + + !-abrindo ficheiro de dados + + open(2,file='HICOLM.md',status='unknown') + + nwr=6 + + write(2,'(i12,e12.4,3i7)')int((ntrialmax-nrelax)/nhist),dtime*tconv,nwr,natom,spctot + + !-preparando Campo de Força + + call ff_prepare + + !-preparando lista de vizinhos de Verlet + + if(nvdw.ne.0.or.ncoul.ne.0)call verlet_list_inter + + if(ntrsff.ne.0)call verlet_list_all + + !-forças iniciais + + if(reuse.eq.0)call ff_modules(encoul,enbond,enbend,entors,envdw,entrsff,virvdw,virbond, & + virbend,virtors,vircoul,virtrsff) + + !-energia potencial + +! enpot=encoul+enbond+enbend+entors+envdw+entrsff + + !-massa total + + mtot=0.d0 + do i=1,natom + mtot=mtot+mass(i) + end do + + return + + end subroutine md_prepare + + subroutine mdloop(mdstp,temp,press,ekinet,enpot) + !*************************************************************************************** + ! Obtencao das variaveis canonicas; * + ! Calculo da energia total; * + ! Atualizacao das lista de vizinhos de Verlet * + ! Impressao das variaveis em ficheiros de saida * + !*************************************************************************************** + + implicit none + + integer mdstp,i,ix + real(8) temp,press + + real(8) virvdw,virbond,virbend,virtors,vircoul,virtrsff + real(8) ekinet,encoul,enbond,enbend,entors,envdw,entrsff,enpot + + !-integrando as variáveis canônicas posição e velocidade + + select case(ensble) + case('nve') + call nve_vv(temp,press,ekinet,encoul,enbond,enbend,entors,envdw,entrsff,virvdw, & + virbond,virbend,virtors,vircoul,virtrsff) + case('nvt') + call nvt_ber_vv(temp,press,ekinet,encoul,enbond,enbend,entors,envdw,entrsff,virvdw, & + virbond,virbend,virtors,vircoul,virtrsff) + case('npt') + call npt_ber_vv(temp,press,ekinet,encoul,enbond,enbend,entors,envdw,entrsff,virvdw, & + virbond,virbend,virtors,vircoul,virtrsff) + end select + + !-calculo da energia potencial + + enpot=encoul+enbond+enbend+entors+envdw+entrsff + + !-imprimindo estrutura + + call geometria + + !-escrevendo variaveis canonicas em arquivo de dados + + if(mdstp.gt.nrelax.and.mod(mdstp-nrelax,nhist).eq.0)then + ix=(mdstp-nrelax)/nhist + write(2,10)ix + write(2,20)(str(i)*econv/rconv**3,i=1,6) + write(2,20)(ix*dtime)*tconv,volume*rconv**3,temp*teconv,& + press*pconv,(ekinet+envdw_corr)*econv,(ekinet+enpot+envdw_corr)*econv,& + (mtot/volume)*mconv/(6.02d-4*rconv**3) + write(2,*) + do i=1,3 + write(2,40)v(i,1)*rconv,v(i,2)*rconv,v(i,3)*rconv + end do + write(2,*) + do i=1,natom + write(2,30)idna(i),atp(i),mass(i)*mconv,parcoul(atp(i),1),xa(i)*rconv, & + ya(i)*rconv,za(i)*rconv + write(2,40)vax(i)*rconv/tconv,vay(i)*rconv/tconv,vaz(i)*rconv/tconv + write(2,40)fax(i)*econv/rconv,fay(i)*econv/rconv,faz(i)*econv/rconv + end do + end if + + !-atualizando a lista de vizinhos de Verlet + + if(mod(mdstp,verlchk).eq.0)then + if(nvdw.ne.0.or.ncoul.ne.0)call verlet_list_inter + end if + + if(ntrsff.ne.0)call verlet_list_all + + return + +10 format(1x,i5) +20 format(6f16.5) +30 format(1x,2i5,5f12.4) +40 format(35x,3f12.4) + + end subroutine mdloop + + subroutine md_print + !************************************************************************* + ! Impressão dos dados de entrada * + !************************************************************************* + implicit none + + integer j + + write(6,*)('#',j=1,70) + write(6,*)'$$$',(' ENTRADA',j=1,8),'$$$' + write(6,*)('#',j=1,70) + write(6,*) + write(6,'(5x,a30)')'Molecular mechanics parameters' + write(6,'(5x,36a1)')('-',j=1,36) + write(6,'(5x,a16,f7.2)')'Temperature (K):',text*teconv + write(6,'(7x,a14,e12.4)')'Pressure (atm):',preext*pconv + write(6,'(12x,a9,a9)')'Ensemble:',ensble + if(ensble.eq.'nvt')then + write(6,'(10x,a11,f5.2)')'Thermostat:',tstat*tconv + elseif(ensble.eq.'npt')then + write(6,'(10x,a11,f5.2)')'Thermostat:',tstat*tconv + write(6,'(10x,a11,2f5.2)')'Barostat:',pstat*tconv,bfactor/pconv + end if + write(6,'(5x,a16,i10)')'ntrialmax:',ntrialmax + write(6,'(5x,a16,i10)')'nrelax:',nrelax + write(6,'(5x,a16,i5)')'reuse:',reuse + write(6,'(5x,a16,f5.3)')'Timestep (ps):',dtime*tconv + write(6,'(5x,a16,2f7.3)')'rcutoff:',rcutoff*rconv,drcutoff*rconv + write(6,'(5x,36a1)')('-',j=1,36) + write(6,*) + + return + + end subroutine md_print + +end module molecular_dynamics diff --git a/SRC/MD/neighbour_list.f90 b/SRC/MD/neighbour_list.f90 new file mode 100644 index 0000000..5a6a627 --- /dev/null +++ b/SRC/MD/neighbour_list.f90 @@ -0,0 +1,164 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module neighbour_list + !***************************************************************************************** + !Atualizacao da lista de vizinhos segundo o método de Verlet * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !***************************************************************************************** + + use input + use estrutura + + integer verlchk,ntrsffstp + + integer, allocatable :: ilist(:,:),ilista(:,:) + integer, allocatable :: nlist(:),nlista(:) + integer, allocatable :: trsffi(:) + + save ntrsffstp,verlchk + +contains + + subroutine neighbour_prepare + !**************************************************************************************** + ! Alocacao de variaveis globais * + !**************************************************************************************** + implicit none + + integer i,numb + + !-valores iniciais + + verlchk=1 + + !-alocando arrays (vizinhos intermoleculares) + + if(nvdw.ne.0.or.ncoul.ne.0)then + numb=0 + do i=1,moltot + numb=numb+(nzmolec(i)-1) + end do + numb=int(0.5*(natom-1)*natom)-numb + allocate(ilist(natom,numb),nlist(natom)) + end if + + !-alocando arrays (vizinhos intramoleculares) + + if(ntrsff.ne.0)then + allocate(ilista(natom,natom),nlista(natom)) + end if + + return + + end subroutine neighbour_prepare + + subroutine verlet_list_all + !**************************************************************************************** + ! Atualizacao a lista de vizinhos segundo o método de Verlet * + !**************************************************************************************** + + implicit none + + integer i,j,nx + real(8) dr,xvz,yvz,zvz,drmax,drx,dry,drz + + !-atualizando lista de vizinhos + + do i=1,natom + nx=1 + do j=1,natom + if(i.eq.j)cycle + call mic(i,j,xvz,yvz,zvz) + dr=sqrt(xvz**2+yvz**2+zvz**2) + if(dr.le.rcutoff)then + ilista(i,nx)=j + nx=nx+1 + end if + nlista(i)=nx-1 + end do + end do + + !-atualizando intervalo + + drmax=0.d0 + do i=1,natom + drx=vax(i)*dtime+0.5d0*fax(i)*dtime**2/mass(i) + dry=vay(i)*dtime+0.5d0*fay(i)*dtime**2/mass(i) + drz=vaz(i)*dtime+0.5d0*faz(i)*dtime**2/mass(i) + dr=sqrt(drx**2+dry**2+drz**2) + drmax=max(drmax,dr) + end do + + if(drmax.ne.0.d0)verlchk=min(verlchk,max(1,int(drcutoff/drmax))) + + return + + end subroutine verlet_list_all + + subroutine verlet_list_inter + !**************************************************************************************** + ! Atualizacao da lista de vizinhos segundo o método de Verlet * + !**************************************************************************************** + implicit none + + integer i,j,ii,jj,nx,ni,nj,nii + real(8) dr,xvz,yvz,zvz,drmax,drx,dry,drz + + !-atualizando lista de vizinhos + + nii=0 + do i=1,moltot + do ii=1,nzmolec(i) + ni=nii+ii + nj=nii+nzmolec(i)+1 + nx=1 + do j=i+1,moltot + do jj=1,nzmolec(j) + call mic(ni,nj,xvz,yvz,zvz) + dr=sqrt(xvz**2+yvz**2+zvz**2) + if(dr.le.rcutoff)then + ilist(ni,nx)=nj + nx=nx+1 + end if + nj=nj+1 + end do + end do + nlist(ni)=nx-1 + end do + nii=nii+nzmolec(i) + end do + + !-atualizando intervalo + + drmax=0.d0 + do i=1,natom + drx=vax(i)*dtime+0.5d0*fax(i)*dtime**2/mass(i) + dry=vay(i)*dtime+0.5d0*fay(i)*dtime**2/mass(i) + drz=vaz(i)*dtime+0.5d0*faz(i)*dtime**2/mass(i) + dr=sqrt(drx**2+dry**2+drz**2) + drmax=max(drmax,dr) + end do + + if(drmax.ne.0.d0)verlchk=min(verlchk,max(1,int(drcutoff/drmax))) + + return + + end subroutine verlet_list_inter + +end module neighbour_list diff --git a/SRC/MD/tersoff_module.f90 b/SRC/MD/tersoff_module.f90 new file mode 100644 index 0000000..4bc7b08 --- /dev/null +++ b/SRC/MD/tersoff_module.f90 @@ -0,0 +1,303 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module tersoff_module + !****************************************************************************************** + ! Contribuicao de diedros para o campo de força: * + ! - Energia potencial; * + ! - Forças atômicas; * + ! - Virial; * + ! - Stress. * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use input + use utils + use estrutura + use alloc_arrays + use neighbour_list + +contains + + subroutine tersoff_convert + !**************************************************************************************** + ! Conversao de unidades de medida: * + ! Unidades de entrada ---> a.u. * + !**************************************************************************************** + + implicit none + + integer i,j + + !-convertendo unidades de medida + + do i=1,spctot + do j=1,spctot + select case(tersoff) + case(1) + partrsff(i,j,1)=partrsff(i,j,1)/rconv + partrsff(i,j,2)=partrsff(i,j,2)/rconv + partrsff(i,j,3)=partrsff(i,j,3)/econv + partrsff(i,j,4)=partrsff(i,j,4)/kconv + partrsff(i,j,6)=partrsff(i,j,6)/rconv + end select + end do + end do + + return + + end subroutine tersoff_convert + + subroutine tersoff_calc(entrsff,virtrsff) + !**************************************************************************************** + ! - Energia potencial; * + ! - Contribuicao para o virial; * + ! - Contribuicao para o stress; * + ! - Forças atômicas. * + !**************************************************************************************** + + implicit none + + integer i,j,ni,nj + real(8) xvz,yvz,zvz,pot + real(8) entrsff,virtrsff + + virtrsff=0.d0 + + do i=1,natom + do j=1,nlista(i) + ni=i + nj=ilista(i,j) + call mic(ni,nj,xvz,yvz,zvz) + call tersoff_force(ni,nj,xvz,yvz,zvz,pot) + entrsff=entrsff+pot + end do + end do + + return + + end subroutine tersoff_calc + + subroutine tersoff_force(i1,i2,xvz,yvz,zvz,pot) + !**************************************************************************************** + ! - Contribuicao para o virial * + ! - Contribuicao para o stress * + ! - Forcas atomicas * + !**************************************************************************************** + + implicit none + + integer i,ii,i1,i2 + real(8) pot,potp,potc,potg1,potg2,potg,dpotp,potp1,potp2 + real(8) xvz,yvz,zvz,dr,prm(4),fbij(3),fbij1(3),fbij2(3),fcij(3),fra(3) + + !-comecando a zica!!!!!!!!!!!!!<------>:( + + do ii=1,4 + prm(ii)=partrsff(atp(i1),atp(i2),ii+2) + end do + + dr=sqrt(xvz**2+yvz**2+zvz**2) + + !-atribuindo termo de restricao da ligação + + call tersoff_restrict(i1,i2,dr,xvz,yvz,zvz,potc,fcij) + + !-atribuindo termo de dependencia angular + + call tersoff_bij(i1,i2,xvz,yvz,zvz,potg1,fbij1) + call tersoff_bij(i2,i1,-xvz,-yvz,-zvz,potg2,fbij2) + + potg=0.5d0*(potg1+potg2) + + do i=1,3 + fbij(i)=0.5d0*(fbij1(i)+fbij2(i)) + end do + + !-VR(r)+bij*VA(r) + + potp1=prm(1)*exp(-sqrt(2.d0*prm(3))*prm(2)*(dr-prm(4)))/(prm(3)-1.d0) + potp2=prm(1)*prm(3)*exp(-sqrt(2.d0/prm(3))*prm(2)*(dr-prm(4)))/(prm(3)-1.d0) + + potp=potp1-potg*potp2 + + !-energia potencial U(r) + + pot=0.5d0*potc*potp + + !-dVR/dr+bij*dVA/dr + + dpotp=-prm(1)*prm(2)*sqrt(2.d0*prm(3))*(exp(-sqrt(2.d0*prm(3))*prm(2)*(dr-prm(4))) & + -potg*exp(-sqrt(2.d0/prm(3))*prm(2)*(dr-prm(4))))/(prm(3)-1.d0) + + !-(1/r)*Vc(r)*(dVR/dr-bij*dVA/dr) + + dpotp=-potc*dpotp/dr + + fra(1)=dpotp*xvz + fra(2)=dpotp*yvz + fra(3)=dpotp*zvz + + !-(VR-bij*VA)*dVc/dr + + fcij(1)=-potp*fcij(1) + fcij(2)=-potp*fcij(2) + fcij(3)=-potp*fcij(3) + + !-Vc(r)*VA(r)*dbij/dr + + do i=1,3 + fbij(i)=potc*potp2*fbij(i) + end do + + !-contribuicao para as forcas atomicas + + fax(i1)=fax(i1)+0.5d0*(-fra(1)-fcij(1)+fbij(1)) + fay(i1)=fay(i1)+0.5d0*(-fra(2)-fcij(2)+fbij(2)) + faz(i1)=faz(i1)+0.5d0*(-fra(3)-fcij(3)+fbij(3)) + + return + + end subroutine tersoff_force + + subroutine tersoff_restrict(i,j,dr,xvz,yvz,zvz,potc,fcij) + !**************************************************************************************** + ! Funcao de corte * + !**************************************************************************************** + + implicit none + + integer i,j + real(8) dr,xvz,yvz,zvz,potc,dpotc,prm(2),fcij(3) + + !-potencial de restricao + + prm(1)=partrsff(atp(i),atp(j),1) + prm(2)=partrsff(atp(i),atp(j),2) + + if(dr.le.prm(1))then + potc=1.d0 + dpotc=0.d0 + elseif(dr.gt.prm(1).and.dr.le.prm(2))then + potc=0.5d0+0.5d0*cos(pi*(dr-prm(1))/(prm(2)-prm(1))) + dpotc=-0.5d0*pi*sin(pi*(dr-prm(1))/(prm(2)-prm(1)))/(prm(2)-prm(1)) + elseif(dr.gt.prm(2))then + potc=0.d0 + dpotc=0.d0 + end if + + dpotc=dpotc/dr + + !-gradiente do termo fc(r) + + fcij(1)=dpotc*xvz + fcij(2)=dpotc*yvz + fcij(3)=dpotc*zvz + + return + + end subroutine tersoff_restrict + + subroutine tersoff_bij(i1,i2,xvz,yvz,zvz,potg,fbij) + !**************************************************************************************** + ! Termo de ajuste da atracao dependente das ligacoes entre vizinhos * + !**************************************************************************************** + + implicit none + + integer i,j,i1,i2,ii,nj + real(8) potg,dpotg,potc,drij(3),drik(3),xvz,yvz,zvz,dr1,dr2,prm(4),fbij(3),fcik(3),fbi(3) + real(8) gtht,sum + + !-valores iniciais + + drij(1)=xvz + drij(2)=yvz + drij(3)=zvz + + dr1=sqrt(drij(1)**2+drij(2)**2+drij(3)**2) + + !-derivadas do termo bij + + do ii=1,4 + prm(ii)=partrsff(atp(i1),atp(i2),ii+6) + end do + + do i=1,3 + fbij(i)=0.d0 + end do + + sum=0.d0 + do i=1,nlista(i1) + nj=ilista(i1,i) + if(nj.eq.i2)cycle + call mic(i1,nj,drik(1),drik(2),drik(3)) + dr2=sqrt(drik(1)**2+drik(2)**2+drik(3)**2) + call tersoff_restrict(i1,nj,dr2,drik(1),drik(2),drik(3),potc,fcik) + call tersoff_bij_gtht(prm,dr1,drij,dr2,drik,gtht,fbi) + do j=1,3 + fbij(j)=fbij(j)-gtht*fcik(j)+potc*fbi(j) + end do + sum=sum+potc*gtht + end do + + !-contribuicao para a energia potencial + + potg=(1.d0+sum)**(-prm(4)) + + !-contribuicao para a forca atomica + + dpotg=-prm(4)*potg**(-1) + + return + + end subroutine tersoff_bij + + subroutine tersoff_bij_gtht(prm,dr1,drij,dr2,drik,gtht,fbi) + !**************************************************************************************** + ! Gradiente do termo de ajuste * + !**************************************************************************************** + + implicit none + + integer i + real(8) dr1,dr2,cost,fa,drij(3),drik(3),prm(4),gtht,fbi(3) + + cost=(drij(1)*drik(1)+drij(2)*drik(2)+drij(3)*drik(3))/(dr1*dr2) + + !-g(theta) + + gtht=prm(1)*(1.d0+(prm(2)/prm(3))**2-prm(3)**2/(prm(3)**2+(1.d0+cost)**2)) + + !-gradiente de g(theta) + + do i=1,3 + fbi(i)=drik(i)/(dr1*dr2)+drij(i)/(dr1*dr2)-cost*(drij(i)/dr1**2+drik(i)/dr2**2) + end do + + fa=2.d0*(1.d0+cost)*prm(1)*prm(3)**2/(prm(3)**2+(1.d0+cost)**2)**2 + + fbi(1)=fa*fbi(1) + fbi(2)=fa*fbi(2) + fbi(3)=fa*fbi(3) + + return + + end subroutine tersoff_bij_gtht + +end module tersoff_module diff --git a/SRC/MD/vdw_module.f90 b/SRC/MD/vdw_module.f90 new file mode 100644 index 0000000..e2618eb --- /dev/null +++ b/SRC/MD/vdw_module.f90 @@ -0,0 +1,231 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module vdw_module + !****************************************************************************************** + ! Contribuicao de Van der Waals para o campo de força: * + ! - Energia potencial; * + ! - Forças atômicas; * + ! - Virial; * + ! - Stress. * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use input + use estrutura + use alloc_arrays + use neighbour_list + + real(8) nvdwstp,envdw_corr,virvdw_corr + + save nvdwstp,envdw_corr,virvdw_corr + +contains + + subroutine vdw_convert + !**************************************************************************************** + ! Conversao de unidades de medida: * + ! Unidades de entrada ---> a.u. * + !**************************************************************************************** + + implicit none + + integer nx,i,j,ii,jj,ni,nj + + !-convertendo parametros de Van der Waals + + do i=1,ntpmax + do j=1,ntpmax + select case(vdw(i,j)) + case(1) + parvdw(i,j,1)=parvdw(i,j,1)/econv + parvdw(i,j,2)=parvdw(i,j,2)/kconv + parvdw(i,j,3)=parvdw(i,j,3)/rconv + case(2) + parvdw(i,j,1)=parvdw(i,j,1)/econv + parvdw(i,j,2)=parvdw(i,j,2)/rconv + end select + end do + end do + + !-calculando qde de Van der Waals e coulomb + + nx=0 + do i=1,moltot + do ii=1,nzmolec(i) + ni=(i-1)*nzmolec(i)+ii + do j=i+1,moltot + do jj=1,nzmolec(j) + nj=(j-1)*nzmolec(j)+jj + nvdwstp=nvdwstp+1 + end do + end do + end do + end do + + return + + end subroutine vdw_convert + + subroutine vdw_calc(envdw,virvdw,ni,nj,xvz,yvz,zvz) + !**************************************************************************************** + ! - Energia potencial; * + ! - Contribuicao para o virial; * + ! - Contribuicao para o stress; * + ! - Forças atômicas. * + !**************************************************************************************** + + implicit none + + integer ni,nj + real(8) xvz,yvz,zvz,fr,pot + real(8) envdw,virvdw + + call vdw_flags(atp(ni),atp(nj),xvz,yvz,zvz,pot,fr) + call vdw_force(ni,nj,xvz,yvz,zvz,fr) + virvdw=virvdw+fr*(xvz**2+yvz**2+zvz**2) + envdw=envdw+pot + + return + + end subroutine vdw_calc + + subroutine vdw_flags(i,j,xvz,yvz,zvz,pot,fr) + !**************************************************************************************** + ! Compontente angular * + !**************************************************************************************** + + implicit none + + integer i,j,ii,ptrm + real(8) pot,fr,xvz,yvz,zvz,dr,prm(3) + + fr=0.d0 + pot=0.d0 + + dr=sqrt(xvz**2+yvz**2+zvz**2) + + ptrm=vdw(i,j) + + select case(ptrm) + case(1) + + do ii=1,3 + prm(ii)=parvdw(i,j,ii) + end do + + pot=prm(1)*(exp(-2.d0*prm(2)*(dr-prm(3))) & + -2.d0*exp(-prm(2)*(dr-prm(3)))) + + fr=2.d0*prm(1)*prm(2)*(exp(-2.d0*prm(2)*(dr-prm(3))) & + -exp(-prm(2)*(dr-prm(3))))/dr + + case(2) + + do ii=1,2 + prm(ii)=parvdw(i,j,ii) + end do + + pot=4.d0*prm(1)*((prm(2)/dr)**12-(prm(2)/dr)**6) + + fr=24.d0*prm(1)*(2.d0*(prm(2)/dr)**12-(prm(2)/dr)**6)/dr**2 + + end select + + return + + end subroutine vdw_flags + + subroutine vdw_force(i,j,xvz,yvz,zvz,fr) + !**************************************************************************************** + ! - Contribuicao para o virial * + ! - Contribuicao para o stress * + ! - Forcas dos atomos i, j, k e n * + !**************************************************************************************** + + implicit none + + integer i,j + real(8) xvz,yvz,zvz,fr + + !-contribuicao para a forca atomica + + fax(i)=fax(i)-fr*xvz + fay(i)=fay(i)-fr*yvz + faz(i)=faz(i)-fr*zvz + fax(j)=fax(j)+fr*xvz + fay(j)=fay(j)+fr*yvz + faz(j)=faz(j)+fr*zvz + + !-contribuição para o stress + + str(1)=str(1)+(fr*xvz)*xvz + str(2)=str(2)+(fr*yvz)*yvz + str(3)=str(3)+(fr*zvz)*zvz + str(4)=str(4)+(fr*zvz)*yvz + str(5)=str(5)+(fr*xvz)*zvz + str(6)=str(6)+(fr*yvz)*xvz + + return + + end subroutine vdw_force + + subroutine vdw_corr() + !**************************************************************************************** + ! - Correcao de Van der Waals para energia e virial * + !**************************************************************************************** + + implicit none + + integer ii,i,j,ptrm + real(8) prm(5),es,vs + + envdw_corr=0.d0 + virvdw_corr=0.d0 + + do i=1,nvdw + do j=i,nvdw + ptrm=vdw(i,j) + select case(ptrm) + case(1) + do ii=1,5 + prm(ii)=parvdw(i,j,ii) + end do + envdw_corr=0.d0 + case(2) + do ii=1,2 + prm(ii)=parvdw(i,j,ii) + end do + es=4.d0*prm(1)*(prm(2)**12-3.d0*(rcutoff*prm(2))**6)/(9.d0*rcutoff**9) + vs=-8.d0*prm(1)*(2.d0*(prm(2)/rcutoff)**6/3.d0-1.d0)*prm(2)**6/rcutoff**3 + envdw_corr=envdw_corr+es*natnp(i)*natnp(j) + virvdw_corr=virvdw_corr+vs*natnp(i)*natnp(j) + end select + envdw_corr=envdw_corr+es + virvdw_corr=virvdw_corr+vs + end do + end do + + envdw_corr=envdw_corr*2*pi/volume + virvdw_corr=virvdw_corr*2*pi/volume + + return + + end subroutine vdw_corr + +end module vdw_module diff --git a/SRC/TB/diagonalize.f90 b/SRC/TB/diagonalize.f90 new file mode 100644 index 0000000..9410831 --- /dev/null +++ b/SRC/TB/diagonalize.f90 @@ -0,0 +1,320 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module diagonalize + !***************************************************************************************** + ! modulo responsavel por resolver o problema de autovalor generalizado * + !***************************************************************************************** + use input + use matriz + + implicit none + + integer norbx + + save norbx + +contains + + subroutine eigsolve_zhegv() + !*************************************************************************************** + ! ???????????????????????????? * + !*************************************************************************************** + implicit none + + integer INFO,LWORK + + real(8), allocatable, dimension(:) :: RWORK + + complex(8), allocatable, dimension(:) :: WORK + + !-alocando arrays + + allocate(WORK(2*norb),RWORK(3*norb-2)) + + call zhegv(1,'N','L',norb,mh,norb,ms,norb,bnd,WORK,-1,RWORK,INFO) + + LWORK=min(int(real(WORK(1))),1000) + + call zhegv(1,'N','L',norb,mh,norb,ms,norb,bnd,WORK,LWORK,RWORK,INFO) + + if(INFO.ne.0)then + write(*,*) 'diagonal: INFO:',INFO,WORK(1) + stop + end if + + return + + end subroutine eigsolve_zhegv + + subroutine eigsolve_dgeev() + !**************************************************************************************** + ! Calculo da equacao matricial * + !**************************************************************************************** + implicit none + + real(8), allocatable, dimension(:,:) :: mhr,msr,ml,mc + + norbx=2*norb + + allocate(mhr(norbx,norbx),msr(norbx,norbx)) + allocate(ml(norbx,norbx)) + allocate(mc(norbx,norbx)) + + call hermitian(mhr,msr) + + call cholesky(msr,ml) + + call pav(mhr,ml,mc) + + call diagonal(mc) + + return + + end subroutine eigsolve_dgeev + + subroutine hermitian(mhr,msr) + !**************************************************************************************** + ! Ttransformacao da matriz complexa em real * + !**************************************************************************************** + implicit none + + integer i,j,ix,jx + + real(8), allocatable, dimension(:,:) :: mhr,msr + + ix=1 + do i=1,norb + jx=1 + do j=1,norb + mhr(ix,jx)=real(mh(i,j)) + msr(ix,jx)=real(ms(i,j)) + jx=jx+1 + end do + do j=1,norb + mhr(ix,jx)=-aimag(mh(i,j)) + msr(ix,jx)=-aimag(ms(i,j)) + jx=jx+1 + end do + ix=ix+1 + end do + + do i=1,norb + jx=1 + do j=1,norb + mhr(ix,jx)=aimag(mh(i,j)) + msr(ix,jx)=aimag(ms(i,j)) + jx=jx+1 + end do + do j=1,norb + mhr(ix,jx)=real(mh(i,j)) + msr(ix,jx)=real(ms(i,j)) + jx=jx+1 + end do + ix=ix+1 + end do + + return + + end subroutine hermitian + + subroutine cholesky(msr,ml) + !***************************************************************************************** + ! Decomposicao L*LT=B usando cholesky * + !***************************************************************************************** + implicit none + + integer i,j,k + real(8) sum,lx + + real(8), allocatable, dimension(:,:) :: msr,ml + + do i=1,norbx + do j=1,norbx + if(abs(msr(i,j)-msr(j,i)).gt.1.d-8)stop 'Cholesky: B is non-symmetric!' + end do + end do + + do i=1,norbx + do j=1,norbx + sum=msr(i,j) + do k=1,i-1 + sum=sum-msr(i,k)*ml(j,k) + end do + if(i.eq.j)then + if(sum.le.0.d0)stop 'Cholesky: B is non-positive-definity!' + lx=sqrt(sum) + ml(i,i)=msr(i,i) + else + ml(j,i)=sum/lx + end if + end do + end do + + return + + end subroutine cholesky + + subroutine pav(mhr,ml,mc) + !**************************************************************************************** + ! Transformacao do problema generalizado A*x=lambda*B*x na equacao de autovalor * + ! (B-1*A)*x=lambda*x * + !**************************************************************************************** + implicit none + + integer i,j,k + real(8) sum + + real(8), allocatable, dimension(:,:) :: my,ml,mc,mhr + + allocate(my(norbx,norbx)) + + do i=1,norbx + do j=1,norbx + my(i,j)=mhr(i,j) + do k=1,j-1 + my(i,j)=my(i,j)-my(i,k)*ml(j,k) + end do + my(i,j)=my(i,j)/ml(j,j) + end do + end do + + do i=1,norbx + do j=1,norbx + sum=my(i,j) + do k=1,i-1 + sum=sum-ml(i,k)*mc(k,j) + end do + mc(i,j)=sum/ml(j,j) + end do + end do + + return + + end subroutine pav + + subroutine diagonal(mc) + !**************************************************************************************** + ! Diagonalizacao da matriz B-1*A-lambda * + !**************************************************************************************** + implicit none + + integer LWORK,INFO,i,j,k,chk + + integer, allocatable, dimension(:) :: ix + + real(8) wrmin,wrmax,wx + + real(8), allocatable, dimension(:) :: WI,WR,VL,VR,WORK + real(8), allocatable, dimension(:,:) :: mc + + LWORK=3*norbx + + allocate(WR(norbx),WI(norbx)) + allocate(VL(norbx),VR(norbx)) + allocate(WORK(LWORK)) + allocate(ix(norbx)) + + call dgeev('N','N',norbx,mc,norbx,WR,WI,VL,norbx,VR,norbx,WORK,LWORK,INFO) + + if(INFO.ne.0)then + write(6,*)'diagonal: INFO:',INFO,WORK(1) + stop + end if + + wrmin=0.d0 + do j=1,norbx + if(WR(j).le.wrmin)then + wrmin=WR(j) + ix(1)=j + end if + end do + + wrmax=wrmin + do j=1,norbx + wrmax=max(wrmax,WR(j)) + end do + + do i=2,norbx + wx=wrmax + do j=1,norbx + if(WR(j).le.wx)then + chk=1 + do k=1,i-1 + if(j.eq.ix(k))chk=0 + end do + if(chk.eq.1)then + ix(i)=j + wx=WR(j) + end if + end if + end do + end do + + do i=1,norb + bnd(i)=WR(ix(2*i)) + end do + + return + + end subroutine diagonal + + subroutine bands(kpt) + !*************************************************************************************** + ! Calculo dos niveis de energia para cada ponto K * + !*************************************************************************************** + implicit none + + integer ix,jx,i,j,p,k,m,pp,l1,l2,m1,m2 + real(8) kpt(3) + + ix=1 + do i=1,natom + do j=1,nlo + l1=lo(j) + do p=1,mlo(j) + m1=mo(j,p) + jx=1 + do k=1,natom + do m=1,nlo + l2=lo(m) + do pp=1,mlo(m) + m2=mo(m,pp) + call neighbourhood(i,k,l1,l2,m1,m2,kpt,ix,jx) + jx=jx+1 + end do + end do + end do + ix=ix+1 + end do + end do + end do + + !-diagonalizando matriz secular + + select case(diagop) + case(1) + call eigsolve_zhegv + case(2) + call eigsolve_dgeev + end select + + return + + end subroutine bands + +end module diagonalize diff --git a/SRC/TB/fitting.f90 b/SRC/TB/fitting.f90 new file mode 100644 index 0000000..ed264b9 --- /dev/null +++ b/SRC/TB/fitting.f90 @@ -0,0 +1,138 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module fitting + !****************************************************************************************** + ! Bandas de energia do calculo DFT com o uso da plataforma SIESTA * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + + use sistema + use input + + implicit none + + integer ihomo,ilumo,nfit,nkptdft + + real(8), allocatable :: bndfit(:,:) + real(8), allocatable :: kptfit(:) + + save ihomo,ilumo + +contains + + subroutine DFT + !*************************************************************************************** + ! Valores de entrada no arquivo bands da plataforma SIESTA * + !*************************************************************************************** + implicit none + + integer i,j,k,iband,bandval,bandcnd + real(8) bottom,top,homo,khomo,gap,lumo,klumo,klen + + data bandval/40/,bandcnd/5/ + + open(8,file='TB.dat',status='unknown') + open(9,file='TB.bands',status='unknown') + + read(9,*)fermi + read(9,*) + read(9,*)bottom,top + read(9,*)nfit,iband,nkptdft + + nfit=nfit*iband + + !-alocando arrays + + allocate(kptfit(nkptdft),bndfit(nkptdft,nfit)) + + homo=bottom + do k=1,nkptdft + read(9,*)kptfit(k),(bndfit(k,i),i=1,nfit) + do i=1,nfit + if(bndfit(k,i).gt.homo.and.bndfit(k,i).le.fermi)then + khomo=kptfit(k) + homo=bndfit(k,i) + ihomo=i + end if + end do + end do + + lumo=top + do k=1,nkptdft + do i=1,nfit + if(bndfit(k,i).lt.lumo.and.bndfit(k,i).ge.fermi)then + klumo=kptfit(k) + lumo=bndfit(k,i) + ilumo=i + end if + end do + end do + + if(homo.lt.fermi)then + gap=lumo-homo + else + gap=0.d0 + end if + + do k=1,nkptdft + do j=1,nfit + bndfit(k,j)=bndfit(k,j)/econv + end do + end do + + fermi=fermi/econv + klen=kptfit(nkptdft) + + !-imprimindo informacoes do calculo DFT + + bandval=min(bandval,ihomo) + bandcnd=min(bandcnd,nfit) + + write(6,*)('#',i=1,70) + write(6,*)'$$$$ ',('DFT ',i=1,15),'$$$$$' + write(6,*)('#',i=1,70) + write(6,*) + write(6,49)' (Bands,K):',nfit,klen + write(6,46)' Fermi level:',fermi*econv + write(6,*) + write(6,45)' Valence band:',ihomo + write(6,46)' (E(k),k):',homo,khomo + write(6,*) + write(6,45)' Conduction band:',ilumo + write(6,46)' (E(k),k):',lumo,klumo + write(6,*) + write(6,46)' GAP:',gap + write(6,*) + + ! -imprimindo bandas de energia do calculo DFT + + do i=1,nkptdft + write(8,'(100f8.3)')kptfit(i),& + ((bndfit(i,j)-fermi)*econv,j=(ihomo-bandval+1),(ihomo+bandcnd)) + end do + + return + +45 format(a25,i10) +46 format(a25,2f10.4) +49 format(a25,i10,f10.4) + + end subroutine DFT + + end module fitting diff --git a/SRC/TB/matriz.f90 b/SRC/TB/matriz.f90 new file mode 100644 index 0000000..b07cea7 --- /dev/null +++ b/SRC/TB/matriz.f90 @@ -0,0 +1,406 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module matriz + + use input + use estrutura + + real(8) dens + + real(8), allocatable, dimension(:) :: bnd + real(8), allocatable, dimension(:,:) :: tpr1, spr1 + real(8), allocatable, dimension(:,:,:) :: onst + + complex(8), allocatable, dimension(:,:) :: ms + complex(8), allocatable, dimension(:,:) :: mh + +contains + + subroutine tb_prepare() + !**************************************************************************************** + ! Alocacao de arrays globais * + !**************************************************************************************** + implicit none + + integer i,j,k,kmx,m1,mlomx,m1mx + + mlomx=0 + kmx=0 + m1mx=0 + do i=1,nlo + do j=1,mlo(i) + do m1=1,npril(i,j) + m1mx=max(m1mx,m1) + end do + mlomx=max(mlomx,j) + end do + do j=1,i + do m1=1,lo(j) + call labels(lo(j),lo(i),m1,k) + kmx=max(k,kmx) + end do + end do + end do + + allocate(ms(norb,norb),mh(norb,norb)) + allocate(tpr1(nparammax,nprllmmax),spr1(nparammax,nprllmmax)) + allocate(onst(lmax,mmax,nprllmmax)) + allocate(bnd(norb)) + + return + + end subroutine tb_prepare + + subroutine neighbourhood(a1,a2,l1,l2,m1,m2,kptt,ix,jx) + !**************************************************************************************** + ! Elementos da matriz secular * + !**************************************************************************************** + implicit none + + integer a1,a2,l1,l2,m1,m2,rx,ry,rz,ix,jx + real(8) xvz,yvz,zvz,kptt(3),arg + complex(8) fk,tmn,smn + + !-calculando os elementos H(alpha1,alpha2) e S(alpha1,alpha2) + + mh(ix,jx)=0.d0 + ms(ix,jx)=0.d0 + do rx=-rxmx,rxmx + do ry=-rymx,rymx + do rz=-rzmx,rzmx + call ccp(a1,a2,rx,ry,rz,xvz,yvz,zvz) + arg=kptt(1)*xvz+kptt(2)*yvz+kptt(3)*zvz + fk=exp(img*arg) + call wigner_matriz(a1,a2,l1,l2,m1,m2,xvz,yvz,zvz,tmn,smn) + mh(ix,jx)=mh(ix,jx)+fk*tmn + ms(ix,jx)=ms(ix,jx)+fk*smn + end do + end do + end do + + return + + end subroutine neighbourhood + + subroutine wigner_matriz(a1,a2,l1,l2,m1,m2,xvz,yvz,zvz,tmn,smn) + !*************************************************************************************** + ! Hoppings e overlaps de acordo com a formula de Wigner * + !*************************************************************************************** + implicit none + + integer, INTENT(IN) :: a1,a2,l1,l2,m1,m2 + real(8), INTENT(IN) :: xvz,yvz,zvz + + integer mx,ml,mll,i,la,lb,ma,mb,m1b,m2b + real(8) dr + complex(8) func,tmn,smn + + la=l1-1 + lb=l2-1 + m1b=m1-(la+1) + m2b=m2-(lb+1) + + dr=sqrt(xvz**2+yvz**2+zvz**2) + + !-calculando os termos onsite + + if(a1.eq.a2)then + if(l1.eq.l2)then + if(m1.eq.m2)then + tmn=osenv(a1,l1,m1,dr) + smn=sprenv(l1,dr) + elseif(m1.ne.m2)then + tmn=0.d0 + smn=0.d0 + end if + elseif(l1.ne.l2)then + tmn=0.d0 + smn=0.d0 + end if + end if + + !-calculando os termos offsite + + if(a1.ne.a2)then + if(m1b.ne.0)then + ml=1 + else + ml=0 + end if + + if(m2b.ne.0)then + mll=1 + else + mll=0 + end if + + tmn=0.d0 + smn=0.d0 + do ma=-ml,ml,2 + do mb=-mll,mll,2 + do mx=-min(la,lb),min(la,lb) + call labels(l1,l2,abs(mx)+1,i) + func=conjg(clmmx(m1b,ma))*clmmx(m2b,mb) & + *conjg(dlmmx(la,ma,mx,xvz,yvz,zvz)) & + *(dlmmx(lb,mb,mx,xvz,yvz,zvz)) + tmn=tmn+func*skv(i,dr) + smn=smn+func*sks(i,dr) + end do + end do + end do + + !-aplicando a propriedade H(l,l')=H(l',l)*(-)**(l+l') + + if(la.gt.lb)then + tmn=tmn*(-1.d0)**(la+lb) + smn=smn*(-1.d0)**(la+lb) + end if + end if + + return + + end subroutine wigner_matriz + + double complex function clmmx(m1,m) + !*************************************************************************************** + ! Coeficientes de transformacao dos harmonicos esfericos para a base real cartesiana * + !*************************************************************************************** + implicit none + + integer, INTENT(IN) :: m,m1 + + if(m1.lt.0)then + if(m.lt.0)then + clmmx=-0.5d0*sqrt(2.d0)*img + elseif(m.gt.0)then + clmmx=-0.5d0*sqrt(2.d0)*img*(-1.d0)**(m1+1) + end if + elseif(m1.eq.0)then + clmmx=1.d0 + elseif(m1.gt.0)then + if(m.lt.0)then + clmmx=0.5d0*sqrt(2.d0) + elseif(m.gt.0)then + clmmx=0.5d0*sqrt(2.d0)*(-1.d0)**(m1) + end if + end if + + return + + end function clmmx + + double complex function dlmmx(l,m,ma,xvz,yvz,zvz) + !*************************************************************************************** + ! Matriz D de rotacao * + !*************************************************************************************** + implicit none + + integer k,kmax,ma,m,l + real(8) xvz,yvz,zvz,dr,rho,fx,fx2 + complex(8) func + + kmax=max(0,ma-m,l-ma,l+m) + + dr=sqrt(xvz**2+yvz**2+zvz**2) + rho=sqrt(xvz**2+yvz**2) + + fx=sqrt(0.5d0*(zvz/dr+1.d0)) + fx2=sqrt(0.5d0*(1.d0-zvz/dr)) + + dlmmx=0.0d0 + do k=0,kmax + func=qklmma(k,l,m,ma)*fx**(2*l+m-ma-2*k) & + *fx2**(2*k-m+ma)*(-1.d0)**(k-m+ma) + dlmmx=dlmmx+func + end do + + dlmmx=dlmmx*(xvz/rho-img*yvz/rho)**m ! Angulo de Euler segundo Eu :) +! dlmmx=dlmmx*(yvz/rho+img*xvz/rho)**m! Angulo de Euler segundo Sakurai :( + + return + + end function dlmmx + + double precision function qklmma(k,l,m,ma) + !**************************************************************************************** + !Funcao q(k,l,m,m1) usada pela matriz D de rotacao * + !**************************************************************************************** + implicit none + + integer k,l,m,ma,i + real(8) pdt,pdt1 + + qklmma=0.d0 + + if((l+m-k).lt.0)goto 1 + if((l-ma-k).lt.0)goto 1 + if((k-m+ma).lt.0)goto 1 + + pdt=1.d0 + do i=1,(l+m) + pdt=pdt*i + end do + do i=1,(l-m) + pdt=pdt*i + end do + do i=1,(l+ma) + pdt=pdt*i + end do + do i=1,(l-ma) + pdt=pdt*i + end do + + pdt1=1.d0 + do i=1,(l+m-k) + pdt1=pdt1*i + end do + do i=1,(l-ma-k) + pdt1=pdt1*i + end do + do i=1,k + pdt1=pdt1*i + end do + do i=1,(k-m+ma) + pdt1=pdt1*i + end do + + qklmma=sqrt(pdt)/pdt1 + +1 return + + end function qklmma + + double precision function osenv(a1,l1,m1,dr) + !**************************************************************************************** + ! Termos onsite da matriz H * + !**************************************************************************************** + implicit none + + integer i + + integer, INTENT(IN) :: l1,a1,m1 + real(8), INTENT(IN) :: dr + + osenv=0.d0 + + if(dr.le.err)then + do i=1,npril(l1,m1) + osenv=osenv+onst(l1,m1,i)*frho(a1)**(2.5*(i-1)) + end do + end if + + return + + end function osenv + + double precision function sprenv(l1,dr) + !**************************************************************************************** + ! Termos onsite da matriz S * + !**************************************************************************************** + implicit none + + integer, INTENT(IN) :: l1 + real(8), INTENT(IN) :: dr + + sprenv=0.d0 + + if(dr.le.err)sprenv=spr(l1) + + return + + end function sprenv + + double precision function skv(i,dr) + !**************************************************************************************** + ! Termos offsite da matriz H * + !**************************************************************************************** + implicit none + + integer, INTENT(IN) :: i + real(8), INTENT(IN) :: dr + + tpr1(i,2)=abs(tpr1(i,2)) + tpr1(i,3)=abs(tpr1(i,3)) + tpr1(i,4)=abs(tpr1(i,4)) + +! skv=(tpr1(i,1)+tpr1(i,3)*dr)*exp(-abs(tpr1(i,2))*dr)*fcutt(dr) +! skv=(tpr1(i,1)*dr**(-tpr1(i,2)))*exp(-tpr1(i,3)*dr)*fcutt(dr) + skv=tpr1(i,1)*dr**(-tpr1(i,4))*exp(-tpr1(i,2)*dr**tpr1(i,3))*fcutt(dr) + + end function skv + + double precision function sks(i,dr) + !*************************************************************************************** + !Funcao que define os termos onsite da matriz S * + !*************************************************************************************** + implicit none + + integer, INTENT(IN) :: i + real(8), INTENT(IN) :: dr + + spr1(i,2)=abs(spr1(i,2)) + spr1(i,3)=abs(spr1(i,3)) + spr1(i,4)=abs(spr1(i,4)) + +! sks=(spr1(i,1)+spr1(i,3)*dr)*exp(-abs(spr1(i,2))*dr)*fcutt(dr) +! sks=(spr1(i,1)*dr**(-spr1(i,2)))*exp(-spr1(i,3)*dr)*fcutt(dr) + sks=spr1(i,1)*dr**(-spr1(i,4))*exp(-spr1(i,2)*dr**spr1(i,3))*fcutt(dr) + + end function sks + + double precision function frho(a1) + !*************************************************************************************** + ! Densidade eletronica do atomo a1 * + !*************************************************************************************** + implicit none + + integer, INTENT(IN) :: a1 + + integer i,rx,ry,rz + real(8) dr,xvz,yvz,zvz + + frho=0.d0 + do i=1,natom + do rx=-3,3 + do ry=-3,3 + do rz=-3,3 + call ccp(i,a1,rx,ry,rz,xvz,yvz,zvz) + dr=sqrt(xvz**2+yvz**2+zvz**2) + frho=frho+exp(-abs(dens)*dr**2)*fcutt(dr) + end do + end do + end do + end do + + return + + end function frho + + double precision function fcutt(dr) + !*************************************************************************************** + ! Ocupacao eletronica de Fermi * + !*************************************************************************************** + implicit none + + real(8) dr + + fcutt=1.d0/(1.d0+exp((dr-rcutt)/lcutt)) + + end function fcutt + +end module matriz diff --git a/SRC/TB/optimizing.f90 b/SRC/TB/optimizing.f90 new file mode 100644 index 0000000..7b90fce --- /dev/null +++ b/SRC/TB/optimizing.f90 @@ -0,0 +1,447 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module optimizing + !****************************************************************************************** + !Modulo de otimizacao dos parametros Slater-Koster * + ! * + !1-ss_sigma * + !2-sp_sigma * + !3-pp_sigma * + !4-pp_pi * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + use sistema + use input + use brillouin + use estrutura + use fitting + use diagonalize + use matriz + + implicit none + + integer kz(nkrlxmax,dkrlxmax),kw,INFOPHM,INFOLMA,npro(lmax),nx + real(8) kptl(nkrlxmax,dkrlxmax,3),FNORMPHM,FNORMLMA + + save FNORMPHM,FNORMLMA,INFOPHM,INFOLMA + +contains + + subroutine optimize + !**************************************************************************************** + ! Escolha de pontos K * + !**************************************************************************************** + implicit none + + integer i,j,k,l,m1,nkpt,i0,chv,nx + real(8) kpt(nkmax,3),mkpt(nbandmax) + real(8) knorm,knorm2,dxpr + + dens=dens0 + + do i=1,nlo + do j=1,mlo(i) + do k=1,npril(i,j) + onst(i,j,k)=onst0(i,j,k) + end do + end do + end do + + do i=1,nparamt + do j=1,nprllm(i) + tpr1(mskt(i),j)=tpr0(mskt(i),j) + spr1(mskt(i),j)=spr0(mskt(i),j) + end do + end do + + if(nopt.eq.0)goto 3 + if(nopt.ge.1)goto 1 + +1 call high_symmetry(1,kpt,mkpt,nkpt) +!------------------------------------- + do j=1,nkrlx + do l=1,dkrlx(j) + chv=1 + i0=0 + knorm2=0.d0 + knorm=0.d0 + do i=1,nkpt + knorm2=knorm2+mkpt(chv)/dband(chv) + if(krlx(j,l).ge.knorm)then + if(krlx(j,l).le.knorm2)then + do k=1,3 + kptl(j,l,k)=kpt(i,k) + end do + kz(j,l)=i + end if + end if + if(i.ge.(i0+dband(chv)))then + chv=chv+1 + i0=i + end if + knorm=knorm2 + end do + end do + end do + + nx=1 + + write(6,*)('#',j=1,70) + write(6,*)'$$ ',('FITTING ',j=1,8),'$$$' + write(6,*)('#',j=1,70) + write(6,*) + write(6,*)' Matrix:',norb + write(6,*) + write(6,43)('-',j=1,27) + +2 call phm + + dxpr=abs(dens-dens0) + + do i=1,nlo + do j=1,mlo(i) + do k=1,npril(i,j) + dxpr=max(dxpr,abs(onst(i,j,k)-onst0(i,j,k))) + end do + end do + end do + + do i=1,nskpar + do j=1,nprllm(i) + if(chk(i).eqv..true.)then + dxpr=max(dxpr,abs(tpr1(msk(i),j)-tpr0(msk(i),j))) + dxpr=max(dxpr,abs(spr1(msk(i),j)-spr0(msk(i),j))) + end if + end do + end do + + dens0=dens + + do i=1,nlo + do j=1,mlo(i) + do k=1,npril(i,j) + onst0(i,j,k)=onst(i,j,k) + end do + end do + end do + + do i=1,nparamt + do j=1,nprllm(i) + tpr0(mskt(i),j)=tpr1(mskt(i),j) + spr0(mskt(i),j)=spr1(mskt(i),j) + end do + end do + + write(6,42)nx,dxpr,FNORMPHM + + if(dxpr.le.1.d-4)goto 3 + + nx=nx+1 + + goto 2 + + !-escrevendo dados em arquivo de saida + +3 write(6,43)('-',j=1,27) + write(6,*) + + nx=1 + do j=1,nlo + npro(nx)=lo(j) + nx=nx+1 + end do + + !-convertendo unidades de medida + + dens0=dens0*(rconv**(-0.5d0)) + + do i=1,nlo + do j=1,mlo(i) + do k=1,npril(i,j) + onst0(i,j,k)=onst0(i,j,k)*econv + end do + end do + end do + + do i=1,nparamt + tpr0(mskt(i),1)=tpr0(mskt(i),1)*econv + tpr0(mskt(i),2)=tpr0(mskt(i),2) + tpr0(mskt(i),3)=tpr0(mskt(i),3)*1.d0/rconv + end do + + do i=1,nparamt + spr0(mskt(i),2)=spr0(mskt(i),2) + spr0(mskt(i),3)=spr0(mskt(i),3)*1.d0/rconv + end do + + !-imprimindo resultados + + nx=0 + do i=1,nparamt + do j=1,nprllm(i) + nx=nx+2 + end do + end do + do i=1,nlo + do j=1,mlo(i) + do k=1,npril(lo(i),mo(i,j)) + nx=nx+1 + end do + end do + end do + + if(chkden.eqv..true.)nx=nx+1 + + if(nopt.ne.0)then + WRITE (6,46) FNORMPHM,INFOPHM + write(6,*) + end if + write(6,*)' Number of parameters:',nx + write(6,*)' Number of adjusted parameters:',nparam + write(6,*) + do i=1,nlo + do j=1,mlo(i) + if(npril(lo(i),mo(i,j)).ge.1)then + write(6,41)'Density:',dens0,chkden + goto 4 + end if + end do + end do +4 write(6,*) + write(6,*)' On-site parameters:' + write(6,43)('-',j=1,21) + write(6,44)'l','m','on-site' + write(6,43)('-',j=1,21) + do i=1,nlo + do j=1,mlo(i) + write(6,47)lo(i)-1,mo(i,j)-lo(i),(onst0(lo(i),mo(i,j),k),k=1,npril(lo(i),mo(i,j))) + end do + end do + write(6,43)('-',j=1,21) + write(6,*) + write(6,*)' Off-site parameters:' + write(6,43)('-',j=1,41) + write(6,45)'l','l','m','offsite' + write(6,43)('-',j=1,41) + do i=1,nlo + do j=1,i + do m1=1,lo(j) + call labels(lo(j),lo(i),m1,k) + write(6,48)lo(j)-1,lo(i)-1,m1-1,chk(k),(tpr0(k,l),l=1,nprllm(k)) + end do + end do + end do + write(6,43)('-',j=1,41) + write(6,*) + write(6,*)' Overlap parameters:' + write(6,43)('-',j=1,41) + write(6,45)'l','l','m','overlap' + write(6,43)('-',j=1,41) + do i=1,nlo + do j=1,i + do m1=1,lo(j) + call labels(lo(j),lo(i),m1,k) + write(6,48)lo(j)-1,lo(i)-1,m1-1,chk(k),(spr0(k,l),l=1,nprllm(k)) + end do + end do + end do + write(6,43)('-',j=1,41) + write(6,*) + + return + +41 format(5x,a23,f12.4,2x,l) +42 format(5x,i4,2(2x,f8.6)) +43 format(5x,43a1) +44 format(5x,2(a2,2x),a8,2x) +45 format(5x,3(a1,2x),3x,a8,2x) +46 FORMAT (5X,31H FINAL L2 NORM OF THE RESIDUALS,D15.7 // & + 5X,15H EXIT PARAMETER,16X,I10 /) +47 format(5x,2(i2,2x),4(f8.4,2x)) +48 format(5x,3(i1,2x),l,2x,10(f8.4,2x)) + + end subroutine optimize + + subroutine phm + !**************************************************************************************** + ! Metodo de minimizacao Powell hibrido fornecido pela biblioteca Minpack * + !**************************************************************************************** + implicit none + + integer i,j,k,nx,nmax,MAXFEV,ML,MU,MODE,NPRINT,INFO,LDFJAC,LR,NFEV + real(8), allocatable, dimension(:) :: WA1,WA2,WA3,WA4 + real(8), allocatable, dimension(:) :: xpr + real(8), allocatable, dimension(:) :: fvec + real(8), allocatable, dimension(:) :: diag + real(8), allocatable, dimension(:) :: rhbrd + real(8), allocatable, dimension(:) :: qtf + real(8), allocatable, dimension(:,:) :: fjac + real(8) XTOL,EPSFCN,FACTOR,ENORM,DPMPAR + + !-alocando arrays + + nmax=nparam + + LR=int(0.5*nmax*(nmax+1)) + + allocate(xpr(nmax),fvec(nmax),fjac(nmax,nmax)) + allocate(rhbrd(LR),qtf(nmax),diag(nmax)) + allocate(WA1(nmax),WA2(nmax),WA3(nmax),WA4(nmax)) + + XTOL=sqrt(DPMPAR(1)) + MAXFEV = 200*(nmax+1) + ML = 1 + MU = 1 + EPSFCN = 500.d0 + MODE = 1 + LDFJAC = nmax + FACTOR = 1.d2 + NPRINT = 1 + + !-definindo variaveis para o processo de otimizacao + + nx=1 + if(chkden.eqv..true.)then + xpr(nx)=dens + nx=nx+1 + end if + + do i=1,nlopar + do j=1,mmopar(i) + do k=1,npril(mlop(i),mmop(i,j)) + xpr(nx)=onst(mlop(i),mmop(i,j),k) + nx=nx+1 + end do + end do + end do + + do i=1,nskpar + do j=1,nprllm(msk(i)) + xpr(nx)=tpr1(msk(i),j) + xpr(nx+1)=spr1(msk(i),j) + nx=nx+2 + end do + end do + + call hybrd(fcn_PHM,nmax,xpr,fvec,XTOL,MAXFEV,ML,MU,EPSFCN,diag,MODE, & + FACTOR,NPRINT,INFO,NFEV,fjac,LDFJAC,rhbrd,LR,qtf,WA1,WA2,WA3,WA4) + + !-redefinindo parametros + + nx=1 + if(chkden.eqv..true.)then + dens=xpr(nx) + nx=nx+1 + end if + + do i=1,nlopar + do j=1,mmopar(i) + do k=1,npril(mlop(i),mmop(i,j)) + onst(mlop(i),mmop(i,j),k)=xpr(nx) + nx=nx+1 + end do + end do + end do + + do i=1,nskpar + do j=1,nprllm(msk(i)) + tpr1(msk(i),j)=xpr(nx) + spr1(msk(i),j)=xpr(nx+1) + nx=nx+2 + end do + end do + + FNORMPHM=ENORM(nmax,FVEC) + + return + + end subroutine phm + + subroutine fcn_PHM(nmax,xpr,fvec,IFLAG) + !**************************************************************************************** + ! Rotina requerida pelo metodo Powell hibrido * + !**************************************************************************************** + implicit none + + integer IFLAG,i,k,l,j,nmax,nx,ll,lx + real(8) xpr(nmax),fvec(nmax),kptt(3) + + if(IFLAG.ne.0)goto 1 + + goto 2 + + !-redefinindo parametros + +1 nx=1 + if(chkden.eqv..true.)then + dens=xpr(1) + nx=nx+1 + end if + + do i=1,nlopar + do j=1,mmopar(i) + do k=1,npril(mlop(i),mmop(i,j)) + onst(mlop(i),mmop(i,j),k)=xpr(nx) + nx=nx+1 + end do + end do + end do + + do i=1,nskpar + do j=1,nprllm(msk(i)) + tpr1(msk(i),j)=xpr(nx) + spr1(msk(i),j)=xpr(nx+1) + nx=nx+2 + end do + end do + + !-checando sistema de equações + + nx=0 + do l=1,nkrlx + do ll=1,dkrlx(l) + nx=nx+1 + end do + end do + + if(nx.ne.nmax)stop 'fcn_PHM: Qty of equations and adjusted variables does not match!' + + !-calculando elemento de matriz H e S + + lx=1 + do l=1,nkrlx + do ll=1,dkrlx(l) + do k=1,3 + kptt(k)=kptl(l,ll,k) + end do + + call bands(kptt) + + fvec(lx)=bndfit(kz(l,ll),nrlx(l))-bnd(ntblx(l)) + + lx=lx+1 + + end do + end do + +2 return + + end subroutine fcn_PHM + +end module optimizing diff --git a/SRC/TB/propriedades.f90 b/SRC/TB/propriedades.f90 new file mode 100644 index 0000000..2952c83 --- /dev/null +++ b/SRC/TB/propriedades.f90 @@ -0,0 +1,338 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module propriedades + !****************************************************************************************** + !Modulo do calculo das propriedades realicionadas com a estrutura eletronica * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !****************************************************************************************** + use sistema + use input + use estrutura + use brillouin + use diagonalize + use matriz + use optimizing + +contains + + subroutine solving + !**************************************************************************************** + ! Flag para o calculo das propriedades eletronicas * + !**************************************************************************************** + implicit none + + ! integer i + + select case(prop) + case('EBAND') + ! write(6,*)('#',i=1,76) + ! write(6,*)'$$$$ ',('PROPRIEDADES',i=1,5),' $$$$' + ! write(6,*)('#',i=1,76) + ! write(6,*) + call ebands ! calculando da energia eletronica + case('BANDS') + ! write(6,*)('#',i=1,76) + ! write(6,*)'$$$$ ',('PROPRIEDADES',i=1,5),' $$$$' + ! write(6,*)('#',i=1,76) + ! write(6,*) + call overlap ! calculando elementos da matriz S + case('BANDS3D') + ! write(6,*)('#',i=1,76) + ! write(6,*)'$$$$ ',('PROPRIEDADES',i=1,5),' $$$$' + ! write(6,*)('#',i=1,76) + ! write(6,*) + call overlap_3d ! calculando elementos da matriz S + case('SURFACE') + ! write(6,*)('#',i=1,76) + ! write(6,*)'$$$$ ',('PROPRIEDADES',i=1,5),' $$$$' + ! write(6,*)('#',i=1,76) + ! write(6,*) + call fermi_surface ! calculando superficie de Fermi + end select + + return + + end subroutine solving + + subroutine overlap + !**************************************************************************************** + ! Diagonalizacao da matriz secular * + !**************************************************************************************** + implicit none + + integer nkpt,i,j,k,nz,nz0,chv + real(8) kpt(nkmax,3),mkpt(nbandmax),kptt(3) + real(8) knorm,dsvres + + open(4,file='bandas.dat',status='unknown') + + !-definindo pontos K + + call high_symmetry(1,kpt,mkpt,nkpt) + + !-calculo das matrizes H e S + + chv=1 + nz0=0 + knorm=0.d0 + dsvres=0.d0 + do nz=1,nkpt + do k=1,3 + kptt(k)=kpt(nz,k) + end do + + !-calculando E(k) + + call bands(kptt) + + knorm=knorm+mkpt(chv)/dband(chv) + + write(4,'(100f8.3)')knorm,((bnd(j)-fermi)*econv,j=1,norb) + + if(nz.ge.(nz0+dband(chv)))then + chv=chv+1 + nz0=nz + end if + + !-interpolando pontos pelo método de Lagrange + + do i=1,nkrlx + do j=1,dkrlx(i) + if(nz.eq.kz(i,j))then + dsvres=dsvres+abs(bndfit(nz,nrlx(i))-bnd(ntblx(i))) + end if + end do + end do + + end do + + if(nopt.ne.0)write(6,100)'Erro(eV):',dsvres/econv + + write(6,*) + + return + +100 format(5x,a9,f12.4) + + end subroutine overlap + + subroutine overlap_3d + !************************************************************************************** + ! Calculo tridimensional da energia da camada de eletronica * + !************************************************************************************** + implicit none + + integer nkpt,i,j,k,l,nz + real(8) kpt(nkmax,3),kptt(3) + + open(3,file='bandas-3d.dat',status='unknown') + + !-definindo pontos K + + nkpt=1 + do i=1,mesh + do j=1,mesh + kpt(nkpt,1)=(i-0.5*mesh)*3.0d0*pi/(a*mesh) + kpt(nkpt,2)=(j-0.5*mesh)*3.0d0*pi/(b*mesh) + kpt(nkpt,3)=2.0d0*pi/b + nkpt=nkpt+1 + end do + end do + + nkpt=nkpt-1 + + !-calculo das matrizes H e S + + do nz=1,nkpt + do k=1,3 + kptt(k)=kpt(nz,k)+kptt0(k) + end do + + !-calculando E(k) + + call bands(kptt) + + write(3,'(11f12.4)')(kptt(i)*kconv,i=1,3),(((bnd(l)-fermi)*econv),l=1,norb) + end do + + return + + end subroutine overlap_3d + + subroutine fermi_surface + !**************************************************************************************** + !Calculo da superficie de Fermi * + !**************************************************************************************** + implicit none + + integer i,j,k,l,nkpt,ix,jx,kx + real(8) kptt(3),kpt(nkmax,3),ek(100),dk1(3),dk2(3),dk3(3) + + open(2,file='HICOLM.BXSF',status='unknown') + + do i=1,3 + dk1(i)=vr(1,i)/mesh + dk2(i)=vr(2,i)/mesh + dk3(i)=vr(3,i)/mesh + end do + + nkpt=1 + do i=0,mesh + do j=0,mesh + do k=0,mesh + kpt(nkpt,1)=(i)*dk1(1)+(j)*dk2(1)+(k)*dk3(1) + kpt(nkpt,2)=(i)*dk1(2)+(j)*dk2(2)+(k)*dk3(2) + kpt(nkpt,3)=(i)*dk1(3)+(j)*dk2(3)+(k)*dk3(3) + nkpt=nkpt+1 + end do + end do + end do + + nkpt=nkpt-1 + + write(2,*)'BEGIN_INFO' + write(2,*)' #' + write(2,*)' # This is a Band_XCRYSDEN-Structure-File' + write(2,*)' # aimed for Visualization of Fermi Surface' + write(2,*)' #' + write(2,*)' # Case: Tight-binding calculation' + write(2,*)' #' + write(2,*)' # Launch as: xcrysden --bxsf TBMC.BXSF' + write(2,*)' #' + write(2,*)' Fermi Energy:',fermi/econv + write(2,*)'END_INFO' + write(2,*) + write(2,*)'BEGIN_BLOCK_BANDGRID_3D' + write(2,*)'Tigh-binding_1st_BZ' + write(2,*)'BEGIN_BANDGRID_3D' + write(2,'(4x,i3)')1 + write(2,'(4x,3i15)')nkpt,nkpt,nkpt + write(2,'(4x,3f15.8)')(kptt0(i)/kconv,i=1,3) + write(2,'(4x,3f15.8)')(vr(1,i)/kconv,i=1,3) + write(2,'(4x,3f15.8)')(vr(2,i)/kconv,i=1,3) + write(2,'(4x,3f15.8)')(vr(3,i)/kconv,i=1,3) + +! do l=1,norb + l=lfermi + write(4,'(4x,a5,i5)')'BAND:',l + + do ix=1,nkpt + kptt(1)=kpt(ix,k) + do jx=1,nkpt + kptt(2)=kpt(jx,k) + do kx=i,nkpt + kptt(3)=kpt(kx,3) + call bands(kptt) + ek(k)=bnd(l) + k=k+1 + end do + write(2,'(4x,3f15.8)')(ek(i),i=1,nkpt) + end do + write(2,*) + end do + !end do + + write(2,*)'END_BANDGRID_3D' + write(2,*)'END_BLOCK_BANDGRID_3D' + + return + + end subroutine fermi_surface + + subroutine ebands + !*************************************************************************************** + ! Calculo da energia eletronica * + !*************************************************************************************** + implicit none + + integer i,j,l,k + real(8) kptt(3),dkx,dky,dkz + real(8) kxshift,kyshift,kzshift,ebs + + real(8), allocatable :: sum(:) + + allocate(sum(norb)) + + !-calculo da integral por simpson + + dkx=(kxmax-kxmin)/mpack(1) + dky=(kymax-kymin)/mpack(2) + dkz=(kzmax-kzmin)/mpack(3) + + kxshift=dkx*ksh(1) + kyshift=dky*ksh(2) + kzshift=dkz*ksh(3) + + do l=1,norb + sum(l)=0.d0 + end do + + do l=1,norb + do k=1,mpack(3) + kptt(3)=kzshift+(k-0.5*mpack(3))*dkz + do j=1,mpack(2) + kptt(2)=kyshift+(j-0.5*mpack(2))*dky + do i=1,mpack(1) + kptt(1)=kxshift+(i-0.5*mpack(1))*dkx + call bands(kptt) + sum(l)=sum(l)+bnd(l)*fermiocp(l) + end do + end do + end do + sum(l)=dkx*dky*dkz*sum(l) + end do + + ebs=0.d0 + do l=1,norb + ebs=ebs+sum(l) + end do + + write(6,'(5x,26a1)')('-',j=1,26) + write(6,'(5x,a1,2(5x,a7))')'l',' Dens ','Energia' + write(6,'(5x,26a1)')('-',j=1,26) + do l=1,natom + write(6,'(5x,i1,4(3x,f9.3))')l,frho(l)*rconv**(1.d0/3.d0),sum(l)*econv + end do + write(6,'(5x,26a1)')('-',j=1,26) + write(6,'(5x,16x,f9.3)')ebs*econv + write(6,*) + + return + + end subroutine ebands + + double precision function fermiocp(i) + !**************************************************************************************** + ! Funcao antisimetrica de Fermi-Dirac * + !**************************************************************************************** + implicit none + + integer i + + if(2*i.le.norb)then + fermiocp=1.d0 + else + fermiocp=0.d0 + end if + + return + + end function fermiocp + +end module propriedades diff --git a/SRC/TB/tight_binding.f90 b/SRC/TB/tight_binding.f90 new file mode 100644 index 0000000..1e9177c --- /dev/null +++ b/SRC/TB/tight_binding.f90 @@ -0,0 +1,254 @@ +! +! This file is part of the HICOLM distribution (https://github.com/flavianowilliams/HICOLM). +! +! Copyright (c) 2019 Flaviano Williams Fernandes. +! +! This program is free software: you can redistribute it and/or modify +! it under the terms of the GNU General Public License as published by +! the Free Software Foundation, version 3. +! +! This program is distributed in the hope that it will be useful, but +! WITHOUT ANY WARRANTY; without even the implied warranty of +! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +! General Public License for more details. +! +! You should have received a copy of the GNU General Public License +! along with this program. If not, see . +! +module tight_binding + !***************************************************************************************** + ! Tight Binding * + ! * + ! Flaviano Williams Fernandes, 05 de dezembro de 2018 * + !***************************************************************************************** + + use input + use fitting + use optimizing + use propriedades + +contains + + subroutine tb(t3) + + implicit none + + real(8) t0,t3 + + !-contagem do tempo absoluto + + call cpu_time(t0) + + !-preparando tight-binding + + call tb_prepare + + !-imprimindo dados de entrada + + call tb_print + + !-convertendo unidades de medida + + call tb_convert + + !-obtendo bandas de energia do calculo DFT + + call DFT + + !-otimizando parametros SK + + call optimize + + !-calculo das propriedades eletronicas + + call solving + + !-contagem do tempo absoluto + + call cpu_time(t3) + + t3=t3-t0 + + return + + end subroutine tb + + subroutine tb_print + !************************************************************************* + ! Impressão dos dados de entrada * + !************************************************************************* + implicit none + + integer i,j,k,l,m1,nx + real(8) t1(3) + + !-parametros do calculo tight-bindind + + nx=0 + do i=1,nlo + do j=1,i + do m1=1,lo(j) + call labels(lo(j),lo(i),m1,k) + do l=1,nprllm(k) + nx=nx+2 + end do + end do + end do + end do + do i=1,nlo + do j=1,mlo(i) + do k=1,npril(lo(i),mo(i,j)) + nx=nx+1 + end do + end do + end do + + do i=1,nlo + do j=1,mlo(i) + if(npril(lo(i),mo(i,j)).gt.1)then + nx=nx+1 + goto 1 + end if + end do + end do + + nx=nx+1 + +1 write(6,'(5x,a36)')'Parametros do calculo Tight-binding:' + write(6,'(5x,36a1)')('-',j=1,36) + write(6,'(5x,a7,i5)')'diagop:',diagop + write(6,'(5x,a7,f5.2)')' rcutt:',rcutt*rconv + write(6,'(5x,a7,f5.2)')' lcutt:',lcutt*econv + write(6,'(5x,36a1)')('-',j=1,36) + write(6,*) + write(6,*)' Orbitais atomicos:' + write(6,'(5x,36a1)')('-',j=1,36) + write(6,'(5x,a3,3x,a2)')'l','m' + write(6,'(5x,36a1)')('-',j=1,36) + do j=1,nlo + write(6,'(6x,i2,5(3x,i2))')(lo(j)-1),((mo(j,k)-1),k=1,mlo(j)) + end do + write(6,'(5x,36a1)')('-',j=1,36) + write(6,*) + write(6,*)' Numero total parametros:',nx + write(6,*) + do i=1,nlo + do j=1,mlo(i) + if(npril(lo(i),mo(i,j)).ge.1)then + write(6,41)'Parametro de densidade:',dens0*rconv**(-0.5d0) + goto 2 + end if + end do + end do +2 write(6,*) + write(6,*)' Termos on-site:' + write(6,43)('-',j=1,21) + write(6,44)'l','m','on-site' + write(6,43)('-',j=1,21) + do i=1,nlo + do j=1,mlo(i) + write(6,47)lo(i)-1,mo(i,j)-lo(i),& + (onst0(lo(i),mo(i,j),k)*econv,k=1,npril(lo(i),mo(i,j))) + end do + end do + write(6,43)('-',j=1,21) + write(6,*) + write(6,*)' Parametros de hoppings:' + write(6,43)('-',j=1,41) + write(6,45)'l','l','m','offsite' + write(6,43)('-',j=1,41) + do i=1,nlo + do j=1,i + do m1=1,lo(j) + call labels(lo(j),lo(i),m1,k) + t1(1)=tpr0(k,1)*econv + t1(2)=tpr0(k,2) + t1(3)=tpr0(k,3)*kconv + write(6,48)lo(j)-1,lo(i)-1,m1-1,(t1(l),l=1,nprllm(k)) + end do + end do + end do + write(6,43)('-',j=1,41) + write(6,*) + write(6,*)' Parametros de overlaps:' + write(6,43)('-',j=1,41) + write(6,45)'l','l','m','overlap' + write(6,43)('-',j=1,41) + do i=1,nlo + do j=1,i + do m1=1,lo(j) + call labels(lo(j),lo(i),m1,k) + t1(1)=spr0(k,1) + t1(2)=spr0(k,2) + t1(3)=spr0(k,3)*kconv + write(6,48)lo(j)-1,lo(i)-1,m1-1,(t1(l),l=1,nprllm(k)) + end do + end do + end do + write(6,43)('-',j=1,41) + write(6,*) + + return + +41 format(5x,a23,f12.4) +43 format(5x,43a1) +44 format(5x,2(a2,2x),a8,2x) +45 format(5x,3(a1,2x),3x,a8,2x) +47 format(5x,2(i2,2x),4(f8.4,2x)) +48 format(5x,3(i1,2x),10(f8.4,2x)) + + end subroutine tb_print + + subroutine tb_convert + !************************************************************************************** + ! Conversão para o sistema padrão u.a. de unidades * + !************************************************************************************** + + implicit none + + integer i,j,k + + err=err*0.5d0/rconv + + !-Parametros SK + + do i=1,lmax + do j=1,2*i+1 + do k=1,npril(i,j) + onst0(i,j,k)=onst0(i,j,k)/econv + end do + end do + end do + + do i=1,nparamt + tpr0(mskt(i),1)=tpr0(mskt(i),1)/econv + tpr0(mskt(i),2)=tpr0(mskt(i),2) + tpr0(mskt(i),3)=tpr0(mskt(i),3)/(1.0d0/rconv) + end do + + do i=1,nparamt + spr0(mskt(i),1)=spr0(mskt(i),1) + spr0(mskt(i),2)=spr0(mskt(i),2) + spr0(mskt(i),3)=spr0(mskt(i),3)/(1.0d0/rconv) + end do + + dens0=dens0/rconv**(-0.5d0) + + lcutt=lcutt/rconv + rcutt=rcutt/rconv + + !-energia de Fermi + + fermi=fermi/econv + + !-parametros no espaço K + + do i=1,3 + kptt0(i)=kptt0(i)/kconv + end do + + return + + end subroutine tb_convert + +end module tight_binding diff --git a/SRC/libraries/liblapack.a b/SRC/libraries/liblapack.a new file mode 100644 index 0000000..370ba3d Binary files /dev/null and b/SRC/libraries/liblapack.a differ diff --git a/SRC/libraries/libminpack.a b/SRC/libraries/libminpack.a new file mode 100644 index 0000000..c5fdfb2 Binary files /dev/null and b/SRC/libraries/libminpack.a differ diff --git a/SRC/libraries/librefblas.a b/SRC/libraries/librefblas.a new file mode 100644 index 0000000..bb7e6cc Binary files /dev/null and b/SRC/libraries/librefblas.a differ diff --git a/SRC/libraries/libtmglib.a b/SRC/libraries/libtmglib.a new file mode 100644 index 0000000..4ebe912 Binary files /dev/null and b/SRC/libraries/libtmglib.a differ diff --git a/SRC/makefile b/SRC/makefile new file mode 100644 index 0000000..ae88393 --- /dev/null +++ b/SRC/makefile @@ -0,0 +1,51 @@ +# Diretorio de instalacao do executavel +ROOT=. +# +# Compilador +FC=gfortran +# +# Instrucoes do compilador +FFLAGS=-fcheck=all -fbacktrace -Wall +# +# bibliotecas +LDFLAGS= -L $(ROOT)/libraries -llapack -lrefblas -lminpack +#===================================================================================== +OBJ_SYS = sistema.o input.o alloc_arrays.o utils.o estrutura.o brillouin.o +# +OBJ_MD = neighbour_list.o vdw_module.o coulomb_module.o \ + bonds_module.o bends_module.o dihedral_module.o \ + tersoff_module.o force_field.o ensemble_nve.o \ + ensemble_nvt.o ensemble_npt.o molecular_dynamics.o +# +OBJ_TB = fitting.o matriz.o diagonalize.o optimizing.o propriedades.o tight_binding.o +# +OBJ_MAIN = outfile.o main.o +#===================================================================================== +ODIR1=$(ROOT)/MAIN +ODIR2=$(ROOT)/MD +ODIR3=$(ROOT)/TB +ODIR4=$(ROOT)/MAIN +# +OBJ1 = $(patsubst %,$(ODIR1)/%,$(OBJ_SYS)) +OBJ2 = $(patsubst %,$(ODIR2)/%,$(OBJ_MD)) +OBJ3 = $(patsubst %,$(ODIR3)/%,$(OBJ_TB)) +OBJ4 = $(patsubst %,$(ODIR4)/%,$(OBJ_MAIN)) +# +$(ODIR1)/%.o: + $(FC) -c $(FFLAGS) -o $@ $(ODIR1)/$*.f90 +# +$(ODIR2)/%.o: + $(FC) -c $(FFLAGS) -o $@ $(ODIR2)/$*.f90 +# +$(ODIR3)/%.o: + $(FC) -c $(FFLAGS) -o $@ $(ODIR3)/$*.f90 +# +$(ODIR4)/%.o: + $(FC) -c $(FFLAGS) -o $@ $(ODIR4)/$*.f90 +# +HICOLM: $(OBJ1) $(OBJ2) $(OBJ3) $(OBJ4) + $(FC) -o $@ $^ $(LDFLAGS) +# +clean: + rm -f $(ODIR1)/*.o $(ODIR2)/*.o $(ODIR3)/*.o $(ODIR4)/*.o *.o *.mod *.dat *.out *.md HICOLM +#========================================================================== diff --git a/UTILS/FTIR/cmmolec.f b/UTILS/FTIR/cmmolec.f new file mode 100644 index 0000000..4d03c0c --- /dev/null +++ b/UTILS/FTIR/cmmolec.f @@ -0,0 +1,211 @@ + module cmmolec +********************************************************************** +* Remocao das projecoes imagem e calculo do centro de massa * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use error + use sizes + use system + use utils +c + implicit none +c + integer natm(molmax,nmax) + integer atmolec(molmax,atmmax) + real(4) rm(fmax,molmax,nmmax,iz),vm(fmax,molmax,nmmax,iz) +c character*8 atmolec(molmax,atmmax) +c + save rm,vm,atmolec,natm +c + contains +c + subroutine molec(check,w,cmserr,cmsprec) +*************************************************************** +* Subrotina que calcula o centro de massa de cada molecula* +* e desliga os efeitos da periodicidade devido as CC * +*************************************************************** +c + implicit none +c + integer i,j,h,p,w,g,t,s,c,cmserr,check + real(kind=4) rsum(2,2,iz),rsq(iz),cmsprec + real(kind=4) mtmol + character*12 mark(nmax) +c + cmsprec=5.e-3 +c + if(check.eq.1)goto 1 +c-------------------------------------------------------------------- +c-atribuindo valores iniciais +c + if(w.eq.1)then + do i=1,atmax + mark(i)='nomodifi' + end do + end if +c-------------------------------------------------------------------- +c-religando sítios da molecula +c + if(w.eq.1)then + s=0 + do h=1,qmol + do p=1,nmolec(h) + g=s+(p-1)*qatom(h) + do j=1,qatom(h) + do i=1,iz + rsq(i)=r(w,g+j,i)-r(w,g+1,i) + if(abs(rsq(i)).gt.l(w,i))mark(g+j)='modified' + end do + call periodicidade(w,rsq) + do i=1,iz + r(w,g+j,i)=rsq(i)+r(w,g+1,i) + end do + end do + end do + s=s+nmolec(h)*qatom(h) + end do + end if +c-------------------------------------------------------------------- +c-desligando CC +c + if(w.gt.1)then + s=0 + do h=1,qmol + do p=1,nmolec(h) + g=s+(p-1)*qatom(h) + do j=1,qatom(h) + do i=1,iz + rsq(i)=r(w,g+j,i)-r(1,g+j,i) + if(abs(rsq(i)).gt.l(w,i))mark(g+j)='modified' + end do + call periodicidade(w,rsq) + do i=1,iz + r(w,g+j,i)=rsq(i)+r(1,g+j,i) + end do + end do + end do + s=s+nmolec(h)*qatom(h) + end do + end if +c-------------------------------------------------------------------- +c-teste da eficiencia do calculo anterior + s=0 + do h=1,qmol + do p=1,nmolec(h) + g=s+(p-1)*qatom(h) + do j=1,qatom(h) + do i=1,iz + if(abs(r(w,g+j,i)-r(w,g+1,i)).gt.l(w,i)) + 1 call erro(1,2,1) + if(w.gt.1)then + if(abs(r(w,g+j,i)-r(w-1,g+j,i)).gt.l(w,i)) + 1 write(*,*)r(w,g+j,i) + if(abs(r(w,g+j,i)-r(w-1,g+j,i)).gt.l(w,i)) + 1 call erro(1,2,1) + end if + end do + end do + end do + s=s+nmolec(h)*qatom(h) + end do +c-------------------------------------------------------------------- +c-imprimindo em REVCON + call revcon(w,mark,2) +c-------------------------------------------------------------------- +c-Calculo do centro de massa +c + do i=1,iz + do h=1,qmol + do p=1,nmolec(h) + rm(w,h,p,i)=0. + vm(w,h,p,i)=0. + end do + end do + do t=1,2 + do j=1,2 + rsum(t,j,i)=0. + end do + end do + end do +c + s=0 + do h=1,qmol + c=0 + do p=1,nmolec(h) + mtmol=0. + g=s+(p-1)*qatom(h) + do j=1,qatom(h) + do i=1,iz + rm(w,h,p,i)=rm(w,h,p,i)+(r(w,g+j,i)*mmol(g+j)) + vm(w,h,p,i)=vm(w,h,p,i)+(v(w,g+j,i)*mmol(g+j)) + end do + atmolec(h,j)=at(g+j) + mtmol=mtmol+mmol(g+j) + end do + do i=1,iz + rsum(1,1,i)=rsum(1,1,i)+(rm(w,h,p,i)) + rsum(2,1,i)=rsum(2,1,i)+(vm(w,h,p,i)) + rm(w,h,p,i)=rm(w,h,p,i)/mtmol + vm(w,h,p,i)=vm(w,h,p,i)/mtmol + end do + c=c+1 + natm(h,c)=c + end do + s=s+nmolec(h)*qatom(h) + end do +c-teste do calculo do centro de massa + do i=1,atmax + do j=1,iz + rsum(1,2,j)=rsum(1,2,j)+(r(w,i,j)*mmol(i)) + rsum(2,2,j)=rsum(2,2,j)+(v(w,i,j)*mmol(i)) + end do + end do + do t=1,1 + do j=1,iz + if(abs(rsum(t,2,j)-rsum(t,1,j)).gt.cmsprec)then + cmserr=cmserr+1 + exit + end if + end do + end do +c-------------------------------------------------------------------- + 1 return +c + end subroutine molec +c + subroutine revcon(w,mark,op) +c + implicit none +c + integer i,j,w,op + character*12 mark(nmax) +c + open(unit=irdd,file="REVCON.xyz",status="unknown") +c + select case(op) + case(1) + write(irdd,'(a37)')'REVCON file generated by surfrag code' + write(irdd,'(2i10)')keyi(1),keyi(2) + write(irdd,'(3f12.4)')l(w,1),keyf(1),keyf(2) + write(irdd,'(3f12.4)')keyf(3),l(w,2),keyf(4) + write(irdd,'(3f12.4)')keyf(5),keyf(6),l(w,3) + do i=1,atmax + write(irdd,'(a8,i10,a31)')at(i),nat(i),mark(i) + write(irdd,'(3e12.4)')(r(w,i,j),j=1,3) + write(irdd,'(3e12.4)')(v(w,i,j),j=1,3) + end do + case(2) + write(irdd,*)atmax + write(irdd,'(a30,i5)')'REVCON file generated by frame',w + do i=1,atmax + write(irdd,'(a8,3f12.4,a31)')at(i),(r(w,i,j),j=1,3),mark(i) + end do + end select +c + close(irdd) +c + return +c + end subroutine revcon +c + end module cmmolec diff --git a/UTILS/FTIR/corr.f b/UTILS/FTIR/corr.f new file mode 100644 index 0000000..f85c4ad --- /dev/null +++ b/UTILS/FTIR/corr.f @@ -0,0 +1,276 @@ + module corr +********************************************************************** +* Cálculo de autocorrelacao * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + use utils + use utilsrange + use system + use cmmolec +c + contains +c + subroutine acfcms(nm,smed,smedi) +c + implicit none +c + integer atm(nmmax) + integer ww,w,n,www + real(kind=4) vs,med,smed(fmax),smedi,dni,nimax + real(kind=4) vm0(nmmax,iz),nm(fmax,molmax,nmmax,iz) +c + smedi=0. + vs=0. +c + www=1 + do ww=d0w,ddw,dtw + smed(www)=0. + www=www+1 + end do +c + w=0 + 1 www=2 + call racfcms(d0w+w,d0w+w,n,atm,nm,vm0,med) + smedi=smedi+med + vs=vs+sqrt(n*med) + do ww=d0w+1,ddw,dtw + call racfcms(ww+w,d0w+w,n,atm,nm,vm0,med) + smed(www)=smed(www)+med + if((ww+w).ge.tmax)goto 2 + www=www+1 + end do + w=w+1 + goto 1 +c + 2 continue +c + smed(1)=smedi + do ww=1,www + smed(ww)=smed(ww)/smedi + end do +c + smedi=smedi/(w+1) +c + dni=dtw + nimax=ddw +c + call smooth(www,dni,nimax,smed) +c + return +c + end subroutine acfcms +c + subroutine racfcms(w,wop,n,atm,nm,vm0,med) + + implicit none + + integer i,j,n,w,wop,ans,g,atm(nmmax) + real(kind=4) vm0(nmmax,iz),med + real(kind=4) nm(fmax,molmax,nmmax,iz),rc(iz) +c + med=0. +c + if(w.eq.wop)then + n=0 + do j=1,nmolec(opm) + do g=1,iz + rc(g)=rm(w,opm,j,g) + end do + call testrange(w,rc,ans) + if(ans.eq.1)then + do i=1,iz + vm0(j,i)=nm(w,opm,j,i) + end do + n=n+1 + atm(n)=j + end if + end do + do j=1,n + do i=1,iz + med=med+nm(w,opm,atm(j),i)*vm0(atm(j),i) + end do + end do + med=med/float(n) + else + do j=1,n + do i=1,iz + med=med+nm(w,opm,atm(j),i)*vm0(atm(j),i) + end do + end do + med=med/float(n) + end if + + return + + end subroutine racfcms +c + subroutine acf(atx,smed,smedi) +c + implicit none +c + integer ww,www,w,n,atm(nmmax) + integer atx + real(kind=4) vs,med,smedi + real(kind=4) v0(nmax,iz),smed(fmax) +c character*8 atx +c + smedi=0. + vs=0. +c + www=1 + do ww=d0w,ddw,dtw + smed(www)=0. + www=www+1 + end do +c + w=0 + 1 www=2 + call racf(d0w+w,d0w+w,atx,n,atm,v0,med) + smedi=smedi+med + vs=vs+sqrt(n*med) + do ww=d0w+1,ddw,dtw + call racf(ww+w,d0w+w,atx,n,atm,v0,med) + smed(www)=smed(www)+med + if((ww+w).ge.tmax)goto 2 + www=www+1 + end do + w=w+1 + goto 1 +c + 2 smed(1)=smedi + do ww=1,www + smed(ww)=smed(ww)/smedi + end do +c + smedi=smedi/(w+1) +c + return +c + end subroutine acf +c + subroutine racf(w,wop,atx,n,atm,v0,med) +c + implicit none +c + integer i,j,n,w,wop + integer atx + integer atm(nmmax),ans,g + real(kind=4) med,rc(iz),v0(nmax,iz) +c character*8 atx +c + med=0. +c + if(w.eq.wop)then + n=0 + do j=1,atmax + if(at(j).eq.atx)then + do g=1,iz + rc(g)=r(w,j,g) + end do + call testrange(w,rc,ans) + if(ans.eq.1)then + do i=1,iz + v0(j,i)=v(w,j,i) + end do + n=n+1 + atm(n)=j + end if + end if + end do + do j=1,n + do i=1,iz + med=med+v(w,atm(j),i)*v0(atm(j),i) + end do + end do + med=med/n + else + do j=1,n + do i=1,iz + med=med+v(w,atm(j),i)*v0(atm(j),i) + end do + end do + med=med/n + end if +c + return +c + end subroutine racf +c + subroutine tcfacf(nm,nt,smed,smedi) +c + implicit none +c + integer dblemol +c + parameter (dblemol=2*nmmax) +c + integer ww,w,n + integer atm(dblemol),nt(fmax) + real(kind=4) v0(dblemol),smed(fmax),nm(fmax,dblemol) + real(kind=4) med,smedi +c + smedi=0. +c + do ww=1,ddw + smed(ww)=0. + end do +c + w=0 + 1 call tcfracf(1+w,1+w,nm,nt,n,atm,v0,med) + smedi=smedi+med + do ww=2,ddw + call tcfracf(ww+w,1+w,nm,nt,n,atm,v0,med) + smed(ww)=smed(ww)+med + if((ww+w).ge.tmax)goto 2 + end do + w=w+1 + goto 1 +c + 2 smed(1)=smedi + do ww=1,ddw + smed(ww)=smed(ww)/smedi + end do +c + smedi=smedi/(w+1) +c + return +c + end subroutine tcfacf +c + subroutine tcfracf(w,wop,nm,nt,n,atm,v0,med) +c + implicit none +c + integer j,n,w,wop,dblemol,nt(fmax) +c + parameter (dblemol=2*nmmax) +c + integer atm(dblemol) + real(kind=4) nm(fmax,dblemol),med,v0(dblemol) +c + med=0. +c + if(w.eq.wop)then + n=0 + do j=1,nt(w) + v0(j)=nm(w,j) + n=n+1 + atm(n)=j + end do + do j=1,nt(w) + med=med+nm(w,atm(j))*v0(atm(j)) + end do + med=med/float(n) + else + do j=1,nt(wop) + med=med+nm(w,atm(j))*v0(atm(j)) + end do + med=med/float(n) + end if +c + return +c + end subroutine tcfracf +c + end module corr diff --git a/UTILS/FTIR/dipmol.f b/UTILS/FTIR/dipmol.f new file mode 100644 index 0000000..ea41a76 --- /dev/null +++ b/UTILS/FTIR/dipmol.f @@ -0,0 +1,171 @@ + module dipmol +********************************************************************** +* Cálculo dos momentos de dipolo molecular e probabilidade * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + use system +c + contains +c + subroutine dipole(dm) +c + implicit none +c + integer nwmax +c + parameter (nwmax=int(nmax/3)) +c + integer i,p,j,w,g,s + real(kind=4) dm(fmax,molmax,nmmax,iz),e,d +c + data e/-1.602176487/,d/4.803/ +c----------------------------------------------------------------------- + s=0 + do i=1,qmol + if(i.lt.opm)s=s+qatom(i)*nmolec(i) + end do +c + do w=1,tmax + do p=1,nmolec(opm) + g=s+(p-1)*qatom(opm) + do j=1,qatom(opm) + do i=1,iz + dm(w,opm,p,i)=0.d0 + end do + end do + end do + do p=1,nmolec(opm) + g=(p-1)*qatom(opm) + do j=1,qatom(opm) + do i=1,iz + dm(w,opm,p,i)=dm(w,opm,p,i)+qat(j)*r(w,g+j,i) +c dm(w,opm,p,i)=dm(w,opm,p,i)+qat(j)*v(w,g+j,i) + end do + end do + end do +c----------------------------------------------------------------------- +c-conversao para Debyes + do p=1,nmolec(opm) + do i=1,iz +c dm(w,opm,p,i)=e*dm(w,opm,p,i)!conversao para SI + dm(w,opm,p,i)=d*dm(w,opm,p,i)!conversao para Debyes + end do + end do + end do +c----------------------------------------------------------------------- + return +c + end subroutine dipole +c + subroutine dipave(dm,integx) +c + implicit none +c + integer mimax,w,p,i +c + parameter (mimax=500) +c + integer n(mimax),nt,nmimax + real(kind=4) dm(fmax,molmax,nmmax,iz),vec(fmax,nmmax) + real(kind=4) int,mi,dmi,ints,s,mimx,prec,dsv,integx + real(kind=4) f(2,mimax),integ(2) + real(kind=4) nn(mimax) +c + common/dipavecalc/ nmimax,dmi,nn +c +c data prec/1.e-3/ + nmimax=mimax +c------------------------------------------------------ +c-modulando os vetores momento de dipolo + mimx=0. +c + do w=1,tmax + do p=1,nmolec(opm) + vec(w,p)=0. + do i=1,3 + vec(w,p)=vec(w,p)+dm(w,opm,p,i)**2 + end do + vec(w,p)=sqrt(vec(w,p)) + mimx=max(mimx,vec(w,p)) + end do + end do +c----------------------------------------------------- +c-calculando os dipolos em intervalos de momento + dmi=mimx/mimax + prec=dmi*1.e-1 +c + mi=0. + do i=1,mimax + n(i)=0 + do w=1,tmax + do p=1,nmolec(opm) + if(vec(w,p).ge.(mi-prec).and.vec(w,p).lt.(mi+prec)) + 1 n(i)=n(i)+1 + end do + end do + mi=mi+dmi + end do +c----------------------------------------------------- +c-contando os momentos dipolo + nt=0 + do i=1,mimax + nt=nt+n(i) + end do +c----------------------------------------------------- +c-normalizando a funcao probabilidade + do i=1,mimax + nn(i)=(float(n(i)))/float(nt) + end do +c + s=0. + do i=2,mimax-1,2 + s=s+nn(i)*4+nn(i+1)*2 + end do + int=dmi*(nn(1)+nn(mimax)+s)/3 +c + do i=1,mimax + nn(i)=nn(i)/int + end do +c-teste da normalizacao + s=0. + do i=1,mimax-1,2 + s=s+nn(i)*4+nn(i+1)*2 + end do + ints=dmi*(nn(1)+nn(mimax)+s)/3 +c----------------------------------------------------- +c-valor medio do momento dipolo e desvio padrao + mi=0. + do i=1,mimax + f(1,i)=nn(i)*mi + f(2,i)=nn(i)*mi**2 + mi=mi+dmi + end do +c + do p=1,2 + s=0 + do i=2,mimax-1,2 + s=s+f(p,i)*4+f(p,i+1)*2 + end do + integ(p)=dmi*(f(p,1)+f(p,mimax)+s)/3 + end do +c + integx=integ(1) + dsv=sqrt(integ(2)-integ(1)**2) +c----------------------------------------------------- + write(*,*)opm,'->',integ(1) +c + write(iwrt,*) + write(iwrt,*)'Momento de dipolo' + write(iwrt,*)('-',i=1,79) + write(iwrt,*)'Valor medio e desvio padrao:',integx,dsv + write(iwrt,'(a21,i10)')'Contagem:',nt + write(iwrt,'(a21,i10)')'Moleculas:',tmax*nmolec(opm) + write(iwrt,'(a21,f10.4)')'Teste da probabilidade:',ints + write(iwrt,*)('-',i=1,79) +c + return +c + end subroutine dipave +c + end module dipmol diff --git a/UTILS/FTIR/error.f b/UTILS/FTIR/error.f new file mode 100644 index 0000000..3b9dbc5 --- /dev/null +++ b/UTILS/FTIR/error.f @@ -0,0 +1,71 @@ + module error +********************************************************************** +* Ceck por erros nos parametros iniciais * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + + contains + + subroutine erro(er,mo,rotn) + + implicit none + + integer er,mo,rotn + + if(mo.eq.1)goto 1 + if(mo.eq.2)goto 2 + + 1 select case(rotn) + case(1) + write(iwrt,*)'molec:' + case(2) + write(iwrt,*)'input:' + case(3) + write(iwrt,*)'dipave:' + case(4) + write(iwrt,*)'tcfstr' + end select + + select case(er) + case(1) + write(iwrt,'(a6,a19)')'Aviso:','Falha em desligar CC' + case(2) + write(iwrt,'(a6,a27)')'Aviso:','Erro na contagem dos atomos' + end select + + goto 3 + + 2 select case(rotn) + case(1) + write(*,*)'molec:' + case(2) + write(*,*)'input:' + case(3) + write(*,*)'dipave:' + case(4) + write(*,*)'tcfstr' + end select + + select case(er) + case(1) + write(*,'(a5,a27)')'Erro:','Falha em desligar CC' + case(2) + write(*,'(a5,a16)')'Erro:','Divisao por zero' + case(3) + write(*,'(a5,a18)')'Erro:','Atomos n/ coincide' + case(4) + write(*,'(a5,a34)')'Erro:','Parametro nao coincide com HISTORY' + case(5) + write(*,'(a5,a27)')'Erro:','Erro na contagem dos atomos' + end select + + stop + + 3 continue + + return + + end subroutine erro + + end module error diff --git a/UTILS/FTIR/ftir.f b/UTILS/FTIR/ftir.f new file mode 100644 index 0000000..045bc49 --- /dev/null +++ b/UTILS/FTIR/ftir.f @@ -0,0 +1,318 @@ + module ftir +********************************************************************** +* Cálculo do espectro vibracional usando transformada de Fourier * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + use utils + use system + use cmmolec + use dipmol + use corr + use tcf +c + contains +c + subroutine infrared(op,strmm,flexmm) +c + implicit none +c + integer pmax,dblemol +c + parameter (pmax=4000) + parameter (dblemol=2*nmmax) +c + integer nimx,w,www,k,i,j,p,op,nx,nt(fmax) + integer atx(atmmax) + real(kind=4) str(fmax,dblemol) + real(kind=4) smedi,smed(fmax),dm(fmax,molmax,nmmax,iz) + real(kind=4) vel(atmmax,fmax),fint(3,pmax),integ(3,atmmax+3,pmax) + real(kind=4) dni,ni,nimax,vol,temp,cte,light,dt,strmm,flexmm + real(kind=4) tcfmed(fmax),flexmed(fmax),dip(fmax) +c character*8 atx(atmmax) +c + data light/3.e-2/,cte/4.553024e5/,dni/1.e-2/ +c + www=ifix((1+(ddw-d0w))/float(dtw)) +c + vol=l(1,1)*l(1,2)*l(1,3) + temp=133 +c + nimax=1/((timestep(2)-timestep(1))*2*dtime*light) + nimx=int(nimax/dni) +c + if(nimx.gt.pmax)then + nimx=pmax + dni=nimax/nimx + end if +c--------------------------------------------------------- +c -calculo FT-IR pelo método ACF do momento de dipolo +c -OBS.: constantes no SI +c--------------------------------------------------------- + write(*,*)'-> FT-IR pelo método ACF do momento de dipolo' +c + call dipole(dm) + call acfcms(dm,dip,smedi) + call fourier(op,dip,fint) +c + cte=cte*smedi/(vol*temp) +c + ni=0. + do k=1,nimx + do i=1,3 + integ(i,1,k)=fint(i,k) !*cte*ni**2 + ni=ni+dni + end do + end do +c--------------------------------------------------------- +c-calculo FT-IR por sítio molecular +c--------------------------------------------------------- + write(*,*)'-> FT-IR por sitio molecular' +c + nx=1 + atx(1)=atmolec(opm,1) + do i=2,qatom(opm) + do j=1,nx + if(atmolec(opm,i).eq.atx(j))goto 2 + end do + nx=nx+1 + atx(nx)=atmolec(opm,i) + 2 continue + end do +c + if(nx.gt.12)nx=12 +c + do p=1,nx + call acf(atx(p),smed,smedi) + call fourier(op,smed,fint) +c + do w=1,www + vel(p,w)=smed(w) + end do +c + do k=1,nimx + do i=1,3 + integ(i,p+3,k)=fint(i,k) + end do + end do + end do +c--------------------------------------------------------- +c -calculo FT-IR do estiramento atomo-atomo +c--------------------------------------------------------- + write(*,*)'-> FT-IR do estiramento sitio-sitio' +c + call tcfstr(str,strmm,nt) +c + do w=1,tmax + if(nt(w).le.1)goto 3 + end do +c + call tcfacf(str,nt,tcfmed,smedi) + call fourier(op,tcfmed,fint) +c + ni=0. + do k=1,nimx + do i=1,3 + integ(i,2,k)=fint(i,k) + ni=ni+dni + end do + end do +c--------------------------------------------------------- +c -calculo FT-IR da flexao atomo-atomo-atomo +c--------------------------------------------------------- + write(*,*)'-> FT-IR angular sitio-sitio-sitio' +c + call tcfflex(str,flexmm,nt) +c + do w=1,tmax + if(nt(w).le.1)goto 4 + end do +c + call tcfacf(str,nt,flexmed,smedi) + call fourier(op,flexmed,fint) +c + ni=0. + do k=1,nimx + do i=1,3 + integ(i,3,k)=fint(i,k) + ni=ni+dni + end do + end do +c---------------------------------------------------------------------- + write(iwrz,'(3x,a1,1x,a4,11x,a6,5x,a7,4x,a9,5x,22(i6,6x))') + 1 '#','Freq','dosvel','stretch','libration',(atx(p),p=1,nx) +c + ni=0. + do k=1,nimx + write(iwrz,'((f9.4,5x,22(f12.5)))')ni,(integ(3,p,k),p=1,nx+3) + ni=ni+dni + end do +c + write(iwtt,'(3x,a1,1x,a4,11x,a6,5x,a7,4x,a9,5x,22(i6,6x))') + 2 '#','Time','dosvel','stretch','libration',(atx(p),p=1,nx) +c + do w=1,www + dt=dtime*float(timestep(w)-timestep(1)) + write(iwtt,'(f9.4,5x,22(f12.5))') + 1 dt,dip(w),tcfmed(w),flexmed(w),(vel(p,w),p=1,nx) + end do +c + write(iwrt,*) + write(iwrt,*)'Cálculo de autocorrelação (TCF)' + write(iwrt,*)('-',i=1,79) + write(iwrt,'(2x,a12,5x,a16)')'Periodo (ps)','autocorrelacao->' + write(iwrt,*)('-',i=1,79) + write(iwrt,'(3x,f10.7,6x,a6,6x,a11,6x,a6,22(3x,i3))') + 1 1/(2*light*nimax),'dosvel','estiramento','flexao',(atx(p),p=1,nx) + write(iwrt,*)('-',i=1,79) + write(iwrt,*) +c + goto 5 +c---------------------------------------------------------------------- + 3 write(iwrz,'(5x,a4,6x,a1,3x,a6,22(2x,a1,3x,a6))') + 2 'Freq',',','dosvel',(',',atx(p),p=1,nx) +c + ni=0. + do k=1,nimx + write(iwrz,'((f9.4,5x,22(a1,f11.5)))') + 1 ni,',',integ(3,1,k),(',',integ(3,p,k),p=4,nx+3) + ni=ni+dni + end do +c + write(iwtt,'(7x,a4,3x,a1,3x,a6,22(2x,a1,3x,a6))') + 2 'Time',',','dosvel',(',',atx(p),p=1,nx) +c + do w=1,www + dt=dtime*float(timestep(w)-timestep(1)) + write(iwtt,'(f11.4,19(1x,a1,f10.4))') + 1 dt,',',dip(w),(',',vel(p,w),p=1,nx) + end do +c + write(iwrt,*) + write(iwrt,*)'Cálculo de autocorrelação (TCF)' + write(iwrt,*)('-',i=1,79) + write(iwrt,'(2x,a12,5x,a16)')'Periodo (ps)','autocorrelacao->' + write(iwrt,*)('-',i=1,79) + write(iwrt,'(3x,f10.7,6x,a6,22(6x,a3))') + 1 1/(2*light*nimax),'dosvel',(atx(p),p=1,nx) + write(iwrt,*)('-',i=1,79) + write(iwrt,*) +c + goto 5 +c------------------------------------------------------------------------ + 4 write(iwrz, + 1 '(5x,a4,6x,a1,3x,a6,2x,a1,2x,a7,22(2x,a1,3x,a6))') + 2 'Freq',',','dosvel',',','stretch',(',',atx(p),p=1,nx) +c + ni=0. + do k=1,nimx + write(iwrz,'((f9.4,5x,22(a1,f11.5)))') + 1 ni,',',integ(3,1,k),',',integ(3,2,k), + 2 (',',integ(3,p,k),p=4,nx+3) + ni=ni+dni + end do +c + write(iwtt, + 1 '(7x,a4,3x,a1,3x,a6,2x,a1,2x,a7,22(2x,a1,3x,a6))') + 2 'Time',',','dosvel',',','stretch',(',',atx(p),p=1,nx) +c + do w=1,www + dt=dtime*float(timestep(w)-timestep(1)) + write(iwtt,'(f11.4,21(1x,a1,f10.4))')dt,',',dip(w), + 1 ',',tcfmed(w),(',',vel(p,w),p=1,nx) + end do +c + write(iwrt,*) + write(iwrt,*)'Cálculo de autocorrelação (TCF)' + write(iwrt,*)('-',i=1,79) + write(iwrt,'(2x,a12,5x,a16)')'Periodo (ps)','autocorrelacao->' + write(iwrt,*)('-',i=1,79) + write(iwrt,'(3x,f10.7,6x,a6,6x,a11,22(6x,a3))') + 1 1/(2*light*nimax),'dosvel','estiramento',(atx(p),p=1,nx) + write(iwrt,*)('-',i=1,79) + write(iwrt,*) +c----------------------------------------------------------------------- + 5 return +c + end subroutine infrared +c + subroutine fourier(op,smed,integ) +c + implicit none +c + integer pmax +c + parameter (pmax=4000) +c + integer k,w,i,op,nimx,www + real(kind=4) light,ni,dni,dt,integ(3,pmax),escc(2),nimax + real(kind=4) essc(2,2),esss(2),smed(fmax),pi +c + data light/3.e-2/,dni/1.e-2/ +c + www=ifix((1+(ddw-d0w))/float(dtw)) +c + pi=acos(-1.0) +c + nimax=1/((timestep(2)-timestep(1))*2*dtime*light) + nimx=int(nimax/dni) +c + if(nimx.gt.pmax)then + nimx=pmax + dni=nimax/nimx + end if +c + call smooth(www,dni,nimax,smed) +c--------------------------------------------------------- + select case(op) +c-calculo da transformada de Fourier discreta -> DFT + case(1) + ni=0. + do k=1,nimx + escc(1)=0. + escc(2)=0. + do w=1,www + dt=(timestep(w)-timestep(1))*dtime!/(www+1) + escc(1)=escc(1)+smed(w)*cos(2*pi*light*ni*dt) + escc(2)=escc(2)+smed(w)*sin(2*pi*light*ni*dt) + end do + integ(1,k)=(escc(1)/www) + integ(2,k)=(escc(2)/www) + integ(3,k)=sqrt(integ(1,k)**2+integ(2,k)**2) + ni=ni+dni + end do +c-calculo da transformada de Fourier pelo metodo Simpson + case(2) + ni=0. + do k=1,nimx + dt=(timestep(www)-timestep(1))*dtime + essc(1,1)=smed(1) + essc(1,2)=smed(www)*cos(2*pi*light*ni*dt) + essc(2,1)=smed(1) + essc(2,2)=smed(www)*sin(2*pi*light*ni*dt) +c + escc(1)=0. + escc(2)=0. + do w=2,www-1 + dt=(timestep(w)-timestep(1))*dtime + esss(1)=smed(w)*cos(2*pi*light*ni*dt) + esss(2)=smed(w)*sin(2*pi*light*ni*dt) + do i=1,2 + if(mod(w,2).eq.0)esss(i)=esss(i)*4 + if(mod(w,2).ne.0)esss(i)=esss(i)*2 + escc(i)=escc(i)+esss(i) + end do + end do + dt=((timestep(www)-timestep(1))*dtime)/www + integ(1,k)=dt*((essc(1,1)+essc(1,2))+escc(1))/(3*acos(-1.0)) + integ(2,k)=dt*((essc(2,1)+essc(2,2))+escc(2))/(3*acos(-1.0)) + integ(3,k)=sqrt(integ(1,k)**2+integ(2,k)**2) + ni=ni+dni + end do + end select +c--------------------------------------------------------- + return +c + end subroutine fourier +c + end module ftir diff --git a/UTILS/FTIR/ftirclass.f b/UTILS/FTIR/ftirclass.f new file mode 100644 index 0000000..356a02c --- /dev/null +++ b/UTILS/FTIR/ftirclass.f @@ -0,0 +1,100 @@ + program ftirclass +********************************************************************** +* Programa FTIR-Class para o calculo do espectro vibracional * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + use system + use cmmolec + use utilsrange + use dipmol + use corr + use tcf + use ftir + use printfile +c + implicit none +c + integer i,w,check,cmserr + real(kind=4) t0,dt,cmsprec + real(kind=4) strmm,flexmm,int,dm(fmax,molmax,nmmax,iz) +c + open(unit=ird,file="TBMD.md",status="old") + open(unit=iwrz,file="infrared.dat",status="unknown") + open(unit=iwtt,file="vacf.dat",status="unknown") + open(unit=iwrx,file="probability.dat",status="unknown") + open(unit=iwrt,file="ftirclass.out",status="unknown") +c + call cpu_time(t0) +c +c&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& + call input +c + write(*,*)'-> calculando CMS e desligando CC' +c + check=0 + cmserr=0 + do w=1,fmax + call coord(check,w) + call molec(check,w,cmserr,cmsprec) + if(check.eq.1)exit + end do +c + if(ddw.gt.tmax)ddw=tmax !acertando o limite máximo p/ ddw +c + write(*,*)'-> Calculo CMS e desligando CC: ok' +c-------------------------------------------------------------------- + dt=dtime*float(timestep(tmax)-timestep(1)) +c + write(iwrt,*) + write(iwrt,*)'Desligando CC?:',' SIM' + write(iwrt,*) + write(iwrt,*)'Parametros do arquivo TBMD.md:' + write(iwrt,*)'-------------------------------------' + write(iwrt,'(a7,2x,i5)')'Frames:',tmax + write(iwrt,'(a14,2x,f9.6)')'Timestep (ps):',dtime + write(iwrt,'(a24,2x,f7.3)')'Intervalo de tempo (ps):',dt + write(iwrt,*)'-------------------------------------' + write(iwrt,*) + write(iwrt,*)'Parametros do calculo de autocorrelacao:' + write(iwrt,*)'----------------------------------------' + write(iwrt,'(a10,i7)')' Inicial:',d0w + write(iwrt,'(a10,i7)')' Amostras:',dtw + write(iwrt,'(a10,i7)')'Intervalo:',ddw + write(iwrt,*)'----------------------------------------' + write(iwrt,*) +c + write(iwrt,*)'Checando calculo do centro de massa!' + write(iwrt,*)'Precisao:',cmsprec + write(iwrt,*) +c + if(cmserr.eq.0)then + write(iwrt,*)'CMS ok!' + else + write(iwrt,*)'CMS fora de precisao (frames):',cmserr + end if +c + write(iwrt,*) +c-------------------------------------------------------------------- +c%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + write(iwrt,*)('%',i=1,79) + write(*,*)'-> calculando espectro FT-IR' + call infrared(1,strmm,flexmm) + write(*,*)'calculo do espectro FT-IR: ok!' +c%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + write(*,*)'-> calculando momento dipolo' + call dipole(dm) + call dipave(dm,int) + write(*,*)'-> calculo do momento dipolo: ok!' +c%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + write(*,*)'-> imprimindo probabilidade' + call prbwrt +c%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +c-imprimindo valores em output + call output(strmm,flexmm,int) +c%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +c-calculando o tempo de CPU + write(iwrt,*)('%',i=1,79) + call info(t0) +c%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + end program ftirclass diff --git a/UTILS/FTIR/makefile b/UTILS/FTIR/makefile new file mode 100644 index 0000000..91ab731 --- /dev/null +++ b/UTILS/FTIR/makefile @@ -0,0 +1,22 @@ +EX = ftirclass +TYPE = seq +SHELL=/bin/bash +#=============================================================== +MOD_MAIN = sizes.o error.o system.o utils.o cmmolec.o +MOD_MOD = utilsrange.o dipmol.o corr.o tcf.o ftir.o printfile.o +MOD_SRC = ftirclass.o +#=============================================================== +intel: + $(MAKE) LD="gfortran -o" FC="gfortran" \ + FFLAGS="-fcheck=all -Wall" \ + EX=$(EX) $(TYPE) +# +seq: $(MOD_MAIN) $(MOD_MOD) $(MOD_SRC) + $(LD) $(EX) $(MOD_MAIN) $(MOD_MOD) $(MOD_SRC) +# +clean: + rm -f $(MOD_MAIN) $(MOD_MOD) $(MOD_SRC) $(EX) *.dat *.out *.mod +#===================================================================== +# Declare dependencies +.o: + $(SHELL) $(FC) $(FFLAGS) $*.f diff --git a/UTILS/FTIR/output.f b/UTILS/FTIR/output.f new file mode 100644 index 0000000..ca8d2ee --- /dev/null +++ b/UTILS/FTIR/output.f @@ -0,0 +1,28 @@ + subroutine output(vacf,strmm,flexmm,int) + + implicit none + + integer ird,irdd,iwrx,iwrt,iwtt,iwrz,iwrh + integer opm,ddw,bnd,flx,i + integer oph(2,10,3),natk(2,10,3),opz(2) + real(kind=4) dni,strcut,vacf,strmm,flexmm,int + + common/acfdata/ opm,opz,oph,ddw,bnd,flx,dni,strcut,natk + common/units/ ird,irdd,iwrh,iwrx,iwtt,iwrz,iwrt + + write(iwrt,*) + write(iwrt,*) + write(iwrt,*)'Valores de saida' + write(iwrt,*)'Molecula',opm + write(iwrt,*)('-',i=1,41) + write(iwrt,'(4x,a8,7x,a7,7x,a5)')'Grandeza','Unidade','Valor' + write(iwrt,*)('-',i=1,41) + write(iwrt,'(a13,4x,a11,4x,f5.2)')'Difusao','x10-5 cm2/s',vacf + write(iwrt,'(a13,4x,a8,7x,f5.2)')'Dipolo','Debye',int + write(iwrt,'(a13,4x,a9,6x,f5.2)')'Estiramento','Angstrom',strmm + write(iwrt,'(a13,4x,a8,6x,f6.2)')'Angulo flexao','Graus',flexmm + write(iwrt,*)('-',i=1,41) + + return + + end subroutine output diff --git a/UTILS/FTIR/prbwrt.f b/UTILS/FTIR/prbwrt.f new file mode 100644 index 0000000..6fc0f21 --- /dev/null +++ b/UTILS/FTIR/prbwrt.f @@ -0,0 +1,36 @@ + subroutine prbwrt +c + implicit none +c + integer maxn,mimax,i,strmax,nmax,flxmax +c + parameter (maxn=500) +c + integer ird,irdd,iwrx,iwrt,iwtt,iwrz,iwrh + real(kind=4) dmi,mi,strmx,dstr,strv,dstr0,dflx0,dflx,flxmx,flxv + real(kind=4) nn(maxn),str(maxn),flx(maxn) +c + common/units/ ird,irdd,iwrh,iwrx,iwtt,iwrz,iwrt + common/dipavecalc/ mimax,dmi,nn + common/tcfstrdata/ strmax,strmx,dstr0,str + common/tcfflexdata/ flxmax,flxmx,dflx0,flx +c----------------------------------------------------- + nmax=min(maxn,min(mimax,min(strmax,flxmax))) +c + dstr=(strmx-dstr0)/nmax + dflx=(flxmx-dflx0)/nmax +c + mi=0. + strv=0.+dstr0 + flxv=0.+dflx0 + do i=1,nmax + write(iwrx,'(3(a4,4x,f7.4,f12.4))') + 1 '1',mi,nn(i),'2',strv,str(i),'3',flxv,flx(i) + mi=mi+dmi + strv=strv+dstr + flxv=flxv+dflx + end do +c----------------------------------------------------- + return +c + end subroutine prbwrt diff --git a/UTILS/FTIR/printfile.f b/UTILS/FTIR/printfile.f new file mode 100644 index 0000000..0effa2f --- /dev/null +++ b/UTILS/FTIR/printfile.f @@ -0,0 +1,69 @@ + module printfile +********************************************************************** +* Imprimindo probabilidades * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + use system +c + contains +c + subroutine prbwrt +c + implicit none +c + integer maxn,mimax,i,strmax,nmax,flxmax +c + parameter (maxn=500) +c + real(kind=4) dmi,mi,strmx,dstr,strv,dstr0,dflx0,dflx,flxmx,flxv + real(kind=4) nn(maxn),str(maxn),flx(maxn) +c + common/dipavecalc/ mimax,dmi,nn + common/tcfstrdata/ strmax,strmx,dstr0,str + common/tcfflexdata/ flxmax,flxmx,dflx0,flx +c----------------------------------------------------- + nmax=min(maxn,min(mimax,min(strmax,flxmax))) +c + dstr=(strmx-dstr0)/nmax + dflx=(flxmx-dflx0)/nmax +c + mi=0. + strv=0.+dstr0 + flxv=0.+dflx0 + do i=1,nmax + write(iwrx,'(3(a4,4x,f7.4,f12.4))') + 1 '1',mi,nn(i),'2',strv,str(i),'3',flxv,flx(i) + mi=mi+dmi + strv=strv+dstr + flxv=flxv+dflx + end do +c----------------------------------------------------- + return +c + end subroutine prbwrt +c + subroutine output(strmm,flexmm,int) + + implicit none +c + integer i + real(kind=4) strmm,flexmm,int +c + write(iwrt,*) + write(iwrt,*) + write(iwrt,*)'Valores de saida' + write(iwrt,*)'Molecula',opm + write(iwrt,*)('-',i=1,41) + write(iwrt,'(4x,a8,7x,a7,7x,a5)')'Grandeza','Unidade','Valor' + write(iwrt,*)('-',i=1,41) + write(iwrt,'(a13,4x,a8,7x,f5.2)')'Dipolo','Debye',int + write(iwrt,'(a13,4x,a9,6x,f5.2)')'Estiramento','Angstrom',strmm + write(iwrt,'(a13,4x,a8,6x,f6.2)')'Angulo flexao','Graus',flexmm + write(iwrt,*)('-',i=1,41) +c + return +c + end subroutine output +c + end module printfile diff --git a/UTILS/FTIR/sizes.f b/UTILS/FTIR/sizes.f new file mode 100644 index 0000000..4b2e939 --- /dev/null +++ b/UTILS/FTIR/sizes.f @@ -0,0 +1,27 @@ + module sizes +********************************************************************** +* Dimensionando arrays * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + public +c******************************************** +c-fmax: limite de frames * +c-nmax: limite de átomos * +c-molmax: limite da quantidade de espécies * +c-nmmax: limite de moléculas * +c-iz: dimensão do espaço vetorial * +c-atmmax: limite de átomos por molécula * +c******************************************** + integer fmax,nmax,iz,molmax,nmmax,atmmax +c + parameter (fmax=1100) + parameter (nmax=6000) + parameter (molmax=4) + parameter (nmmax=2000) + parameter (atmmax=200) + parameter (iz=3) +c + integer ird,irdd,iwrx,iwrt,iwtt,iwrz,iwrh + parameter (ird=1,irdd=2,iwrx=3,iwtt=4,iwrz=8,iwrh=6,iwrt=7) +c + end module sizes diff --git a/UTILS/FTIR/system.f b/UTILS/FTIR/system.f new file mode 100644 index 0000000..d3f7c89 --- /dev/null +++ b/UTILS/FTIR/system.f @@ -0,0 +1,234 @@ + module system +********************************************************************** +* Leitura das variaveis atomicas e parametros de entrada * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + use error +c + implicit none +c + integer qmol,nmolec(molmax),qatom(molmax) + integer opm,opx,ddw,d0w,dtw,bnd,flx,opsmth + integer nat(nmax),atmax,tmax,timestep(fmax),keyi(5) + integer oph(2,10,3),natk(2,10,3),opz(2),at(nmax),att + real(kind=4) strcut,qat(nmax),rmin,rmax,mmol(nmax) + real(kind=4) r(fmax,nmax,iz),v(fmax,nmax,iz),a(fmax,nmax,iz) + real(kind=4) l(fmax,iz),keyf(8),dtime,dsmth +c + save qmol,nmolec,qatom + save nat,atmax,tmax,r,v,a,at,l + save dtime,timestep,keyf,keyi + save opm,oph,bnd,flx,strcut,natk,opz,qat + save d0w,dtw,ddw + save opx,rmin,rmax,att + save opsmth,dsmth +c + contains +c + subroutine input +c + implicit none +c + integer i +c + write(*,*)'Quantidade de especies' + read(*,*)qmol + + write(*,*)'Quantidade de atomos e moleculas por especie' +c + do i=1,qmol + read(*,*)qatom(i),nmolec(i) + end do +c + call opinit() +c + write(iwrt,'(10x,14a3)')('ITA',i=1,14) + write(iwrt,'(7x,a43)')'Calculo do sistema solvente-substrato' + write(iwrt,'(10x,14a3)')('ITA',i=1,14) + write(iwrt,*) + write(iwrt,*)'Parametros de entrada:' + write(iwrt,*) + write(iwrt,*)'Quantidade de especies:',qmol + write(iwrt,*) + write(iwrt,'(a7,a15,a15,a15)') + 1 'Especie','atom/molec','moleculas' + write(iwrt,*)('-',i=1,35) + + do i=1,qmol + write(iwrt,'(i4,i13,i18,f17.4)')i,qatom(i),nmolec(i) + end do + + write(iwrt,*)('-',i=1,35) +c + return + + end subroutine input +c + subroutine coord(check,w) +c + implicit none +c + integer w,i,j,k,h,p,s,g,check + character*20 lixc +c + if(w.eq.1)then + read(ird,'(a12,f12.4,a7,i7,a7)')lixc,dtime,lixc,atmax,lixc + keyi(1)=2 + keyi(2)=2 + end if +c + read(ird,100,end=1)timestep(w) +c + read(ird,*) + read(ird,*) + read(ird,*) + read(ird,300)l(w,1),keyf(1),keyf(2) + read(ird,300)keyf(3),l(w,2),keyf(4) + read(ird,300)keyf(5),keyf(6),l(w,3) +c + read(ird,*) +c + k=1 + do i=1,atmax + read(ird,400)lixc,at(i),mmol(i),qat(i),(r(w,i,j),j=1,iz) + read(ird,300)(v(w,i,j),j=1,iz) + read(ird,300)(a(w,i,j),j=1,iz) + nat(i)=k + k=k+1 + end do +c + k=k-1 +c-------------------------------------------------------------------- +c-teste da quantidade de atomos + s=0 + do h=1,qmol + do p=1,nmolec(h) + g=s+(p-1)*qatom(h) + do j=1,qatom(h) + i=g+j + end do + end do + s=s+nmolec(h)*qatom(h) + end do +c + if(i.ne.k)call erro(3,2,2) +c + tmax=w +c + goto 2 +c + 1 check=1 + + 2 return +c + 100 format(1x,i5) +c 200 format(6a16) + 300 format(35x,3f12.4) + 400 format(1x,a5,i5,5f12.4) +c + end subroutine coord +c + subroutine opinit() +c + implicit none +c + integer i,j +c-------------------------------------------------------- +c-atribuindo valores iniciais + att=1 + dsmth=0. +c-------------------------------------------------------- + write(*,*)'Calculo ACF!' + write(*,*)'Molecula de referencia:' + read(*,*)opm +c + write(*,*)'Controle do calculo ACF:' + write(*,*)'Inicial, amostras, intervalo amostral:' + read(*,*)d0w,dtw,ddw +c + write(*,*)'Range:' + write(*,*)'None? -> 1' + write(*,*)'Eixo z? -> 2' + write(*,*)'Pesonalizado? -> 3' + read(*,*)opx +c + if(opx.eq.2)then + write(*,*)'Alcance minimo e maximo:' + read(*,*)rmin,rmax + end if +c + if(opx.eq.3)then + write(*,*)'Atomo de referencia e alcance min. e max.:' + read(*,*)att,rmin,rmax + end if +c + write(*,*)'Estiramento pelo metodo TCF!' + write(*,*)'Quantidade a ser analisada' + read(*,*)bnd + + write(*,*)'Intermolecular? -> 1' + write(*,*)'Intramolecular? -> 2' + read(*,*)opz(1) +c + write(*,*)'Moleculas e atomos da coordenada relativa:' +c + do i=1,bnd + write(*,*)'->',i + if(opz(1).eq.1)then + do j=1,2 + read(*,*)oph(1,i,j),natk(1,i,j) + end do + else + read(*,*)(natk(1,i,j),j=1,2) + do j=1,2 + oph(1,i,j)=opm + end do + end if + end do +c + write(*,*)'Deformacao pelo metodo TCF!' + write(*,*)'Quantidade a ser analisada' + read(*,*)flx +c + write(*,*)'Intermolecular? -> 1' + write(*,*)'Intramolecular? -> 2' + read(*,*)opz(2) +c + do i=1,flx + write(*,*)'->',i + if(opz(2).eq.1)then + write(*,*)'Moleculas e atomos da coordenada relativa' + do j=1,3 + read(*,*)oph(2,i,j),natk(2,i,j) + end do + else + write(*,*)'Atomos da coordenada relativa' + read(*,*)(natk(2,i,j),j=1,3) + do j=1,3 + oph(2,i,j)=opm + end do + end if + end do +c + write(*,*)'Distancia maxima de estiramento:' + read(*,*)strcut +c + write(*,*)'Escolha da funcao janela para o metodo de suavizacao' + write(*,*)'1 -> retangular' + write(*,*)'2 -> Poisson' + write(*,*)'3 -> Hann-Poisson' + write(*,*)'4 -> Cauchy' + write(*,*)'5 -> Gaussiana' + read(*,*)opsmth +c + if(opsmth.ne.1)then + write(*,*)'Parametro de decaimento' + read(*,*)dsmth + end if +c + return +c + end subroutine opinit +c + end module system diff --git a/UTILS/FTIR/tcf.f b/UTILS/FTIR/tcf.f new file mode 100644 index 0000000..7b91647 --- /dev/null +++ b/UTILS/FTIR/tcf.f @@ -0,0 +1,398 @@ + module tcf +********************************************************************** +* Cálculo TCF dos estiramento e deformação * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + use system + use cmmolec + use utilsrange +c + contains +c + subroutine tcfstr(sqtstr,strmm,n) +c + implicit none +c + integer strmax,dblemol,t0,nt,pp,ppp,ans,ans1(nmax),ans2(nmax) + integer n(fmax) +c + parameter (dblemol=2*nmmax,strmax=500) +c + integer w,j,i,k,p,g,gg,t,s,ss,strmmax + real(kind=4) sqtstr(fmax,dblemol),str(dblemol,iz) + real(kind=4) strmm,strm,strmx,dsv,dstr0 + real(kind=4) nn(strmax),rc1(iz),rc2(iz),rx(2,nmax,iz) +c + common/tcfstrdata/ strmmax,strmx,dstr0,nn +c + write(*,*)'-> Calculo do Estiramento' +c + strmmax=strmax +c--------------------------------------------------------- +c-calculo da coordenada relativa + nt=0 + dstr0=0. + strmx=0. + do w=1,tmax + n(w)=1 + select case(opz(1)) + case(1) + do j=1,bnd + s=0 + ss=0 + do i=1,qmol + if(i.lt.oph(1,j,1))s=s+qatom(i)*nmolec(i) + if(i.lt.oph(1,j,2))ss=ss+qatom(i)*nmolec(i) + end do +c--------------------------------------------------------- +c-contagem de atomos na regiao z1',strmm,dsv + write(*,*)'Estiramento ->',strmm +c--------------------------------------------------------- +c-recalculando arrays + do w=1,tmax + strm=0. + if(n(w).gt.0)then + do j=1,n(w) + strm=strm+sqtstr(w,j) + end do + strm=strm/float(n(w)) + do j=1,n(w) + sqtstr(w,j)=sqtstr(w,j)-strm + end do + end if + end do +c--------------------------------------------------------- + return +c + end subroutine tcfstr +c + subroutine tcfflex(sqtstr,strmm,n) + + implicit none +c + integer w,j,i,k,p,g,gg,ggg,z,s,ss,sss,t,q,nt + integer dblemol,strmax,strmmax +c + parameter (dblemol=2*nmmax,strmax=500) +c + integer n(fmax) + integer ans1,ans2 + real(kind=4) sqtstr(fmax,dblemol),str(2,dblemol,iz) + real(kind=4) strmm,strm,strx,dsv,strmx,dflx0 + real(kind=4) nn(strmax),rc1(iz),rc2(iz) +c + common/tcfflexdata/ strmmax,strmx,dflx0,nn +c + write(*,*)'-> Calculo da deformacao!' +c + strmmax=strmax +c--------------------------------------------------------- +c-calculo dos vetores coplanares + nt=0 + dflx0=-1. + strmx=1. + do w=1,tmax + n(w)=1 + select case(opz(2)) + case(1) + do j=1,flx + s=0 + ss=0 + sss=0 + do i=1,qmol + if(i.lt.oph(2,j,1))s=s+qatom(i)*nmolec(i) + if(i.lt.oph(2,j,2))ss=ss+qatom(i)*nmolec(i) + if(i.lt.oph(2,j,3))sss=sss+qatom(i)*nmolec(i) + end do + do p=1,nmolec(oph(2,j,2)) + gg=ss+(p-1)*qatom(oph(2,j,2)) + do k=1,nmolec(oph(2,j,1)) + g=s+(k-1)*qatom(oph(2,j,1)) + strx=0. + do i=1,iz + strx=strx+(r(w,g+natk(2,j,1),i) + 1 -r(w,gg+natk(2,j,2),i))**2 + end do + strx=sqrt(strx) + if(strx.gt.strcut)goto 2 + do t=k+1,nmolec(oph(2,j,3)) + ggg=sss+(t-1)*qatom(oph(2,j,3)) + strx=0. + do i=1,iz + strx=strx+(r(w,ggg+natk(2,j,3),i) + 1 -r(w,gg+natk(2,j,2),i))**2 + end do + strx=sqrt(strx) + if(strx.gt.strcut)goto 1 + do i=1,iz + rc1(i)=rm(w,oph(1,j,1),t,i) + rc2(i)=rm(w,oph(1,j,2),t,i) + end do + call testrange(w,rc1,ans1) + call testrange(w,rc2,ans2) + if(ans1*ans2.eq.1)then + do i=1,iz + str(1,n(w),i)=r(w,g+natk(2,j,1),i) + 1 -r(w,gg+natk(2,j,2),i) + str(2,n(w),i)=r(w,ggg+natk(2,j,3),i) + 1 -r(w,gg+natk(2,j,2),i) + end do + n(w)=n(w)+1 + end if + 1 continue + end do + 2 continue + end do + end do + end do + case(2) + do j=1,flx + do p=1,nmolec(oph(2,j,1)) + g=(p-1)*qatom(oph(2,j,1)) + do k=1,iz + rc1(k)=rm(w,oph(1,j,1),p,k) + end do + call testrange(w,rc1,ans1) + if(ans1.eq.1)then + do z=1,2 + do i=1,iz + str(z,n(w),i)=r(w,g+natk(2,j,2*z-1),i) + 1 -r(w,g+natk(2,j,2),i) + end do + end do + n(w)=n(w)+1 + end if + end do + end do + end select +c + n(w)=n(w)-1 +c + nt=nt+n(w) +c--------------------------------------------------------- +c-calculo do angulo entre vetores + do j=1,n(w) + sqtstr(w,j)=0. + do i=1,iz + sqtstr(w,j)=sqtstr(w,j)+str(1,j,i)*str(2,j,i) + end do + do q=1,2 + strx=0. + do i=1,iz + strx=strx+str(q,j,i)**2 + end do + strx=sqrt(strx) + sqtstr(w,j)=sqtstr(w,j)/strx + end do + end do +c--------------------------------------------------------- + end do +c + write(*,*)nt,'arrays' +c--------------------------------------------------------- +c-calculo do desvio padrao e valor medio +c call desvio(n(tmax)*tmax,valy,dsv,strmm) +c +c strmm=strmm/(float(n*tmax)) +c strmm=acos(strmm)*180/acos(-1.d0) +c dsv=acos(dsv)*180/acos(-1.d0) +c +c--------------------------------------------------------- +c-calculo da probabilidade + call tcfprb(strmax,dflx0,strmx,sqtstr,n,nn,strmm,dsv) +c + strmm=acos(strmm)*180/acos(-1.) + dsv=acos(dsv)*180/acos(-1.) +c + write(iwrt,*)'Flexao ->',strmm,dsv + write(*,*)'Flexao ->',strmm +c--------------------------------------------------------- +c-recalculando arrays + do w=1,tmax + strm=0. + if(n(w).gt.0)then + do j=1,n(w) + strm=strm+sqtstr(w,j) + end do + strm=strm/float(n(w)) + do j=1,n(w) + sqtstr(w,j)=sqtstr(w,j)-strm + end do + end if + end do +c--------------------------------------------------------- + return + + end subroutine tcfflex +c + subroutine tcfprb(strmax,dstr0,strmx,sqtstr,n,nn,vm,dsv) + + implicit none + + integer strmax,i,j,w,nt,p,dblemol +c + parameter (dblemol=2*nmmax) +c + integer strprb(strmax),n(fmax) + real(kind=4) prec,dstr,strmx,strv,sm,int,vm,dsv,dstr0 + real(kind=4) sqtstr(fmax,dblemol),f(2,strmax),integ(2) + real(kind=4) nn(strmax) +c--------------------------------------------------------- +c-calculo da probabilidade + dstr=(strmx-dstr0)/strmax + prec=dstr*5.e-1 + strv=0.+dstr0 + do i=1,strmax + strprb(i)=0 + do w=1,tmax + do j=1,n(w) + if(sqtstr(w,j).ge.(strv-prec))then + if(sqtstr(w,j).lt.(strv+prec))then + strprb(i)=strprb(i)+1 + end if + end if + end do + end do + strv=strv+dstr + end do +c--------------------------------------------------------- +c-contando as distancias relativas + nt=0 + do i=1,strmax + nt=nt+strprb(i) + end do +c--------------------------------------------------------- +c-normalizando a função probabilidade + do i=1,strmax + nn(i)=(float(strprb(i))/float(nt)) + end do +c + sm=0. + do i=2,strmax-1,2 + sm=sm+nn(i)*4+nn(i+1)*2 + end do + int=dstr*(nn(1)+nn(strmax)+sm)/3 +c + do i=1,strmax + nn(i)=nn(i)/int + end do +c--------------------------------------------------------- +c-calculo do valor médio de estiramento e desvio padrao +c call desvio(n(tmax)*tmax,valy,dsv,strmm) + strv=0.+dstr0 + do i=1,strmax + f(1,i)=nn(i)*strv + f(2,i)=nn(i)*strv**2 + strv=strv+dstr + end do +c + do p=1,2 + sm=0. + do i=2,strmax-1,2 + sm=sm+f(p,i)*4+f(p,i+1)*2 + end do + integ(p)=dstr*(f(p,1)+f(p,strmax)+sm)/3 + end do +c + vm=integ(1) + dsv=sqrt(integ(2)-integ(1)**2) +c + return +c + end subroutine tcfprb +c + end module tcf diff --git a/UTILS/FTIR/utils.f b/UTILS/FTIR/utils.f new file mode 100644 index 0000000..34a13e8 --- /dev/null +++ b/UTILS/FTIR/utils.f @@ -0,0 +1,125 @@ + module utils +********************************************************************** +* Subrotinas úteis para o pacote FTIR-Class * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + use system +c + contains +c + subroutine smooth(www,dni,nimax,smed) +c + implicit none +c + integer i,op,www + real(kind=4) smed(fmax),ni,dni,nimax,pi,phi + real(kind=4) d +c + op=opsmth + d=dsmth +c + pi=acos(-1.0) +c + ni=0.+dni + select case(op) + case(1) !retangular + do i=2,www + smed(i)=smed(i)*1.0 + end do + case(2) !Poisson + do i=2,www + smed(i)=smed(i)*exp(-2.*d*abs(ni)/nimax) + ni=ni+dni + end do + case(3) !Hann-Poisson + do i=2,www + phi=pi*ni/nimax + smed(i)=smed(i)*.5*(1+cos(2.*phi))*exp(-2.*d*abs(ni)/nimax) + end do + case(4) !Cauchy + do i=2,www + smed(i)=smed(i)/(1+(2.*d*ni/nimax)**2) + end do + case(5) !Gaussiana + do i=2,www + smed(i)=smed(i)*exp(-.5*(2.*d*ni/nimax)**2) + end do + end select +c + return +c + end subroutine smooth +c + subroutine periodicidade(w,img) + + implicit none + + integer w + real(kind=4) aaa,bbb,ccc,img(iz) + + aaa=1.0/l(w,1) + bbb=1.0/l(w,2) + ccc=1.0/l(w,3) +c + img(1)=img(1)-l(w,1)*nint(aaa*img(1)) + img(2)=img(2)-l(w,2)*nint(bbb*img(2)) + img(3)=img(3)-l(w,3)*nint(ccc*img(3)) +c + return + + end subroutine periodicidade +c + subroutine desvio(nmax,valy,dsv,md) + + implicit none + + integer ymax,nmax,i + + parameter (ymax=10000000) + + real (kind=4) valy(ymax) + real (kind=4) sum,md,dsv + + md=0. + do i=1,nmax + md=md+valy(i) + end do + + md=md/float(nmax) + + sum=0. + do i=1,nmax + sum=sum+(valy(i)-md)**2 + end do + + dsv=sqrt(sum/float(nmax-1)) + + return + + end subroutine desvio +c + subroutine info(t0) + + implicit none + + real(kind=4) t0,tf + character(10) host,time + character(8) date + + call date_and_time(Date=date) + call date_and_time(TIME=time) + call hostnm(host) + call cpu_time(tf) + + write(iwrt,*) + write(iwrt,*)('Host: '),host + write(iwrt,'(''Date: '',2x,a8)')date + write(iwrt,'(''Time: '',2x,a10)')time + write(iwrt,'(''Tempo estimado = '',f8.2,'' segundos'')')tf-t0 + + return + + end subroutine info +c + end module utils diff --git a/UTILS/FTIR/utilsrange.f b/UTILS/FTIR/utilsrange.f new file mode 100644 index 0000000..81623bb --- /dev/null +++ b/UTILS/FTIR/utilsrange.f @@ -0,0 +1,74 @@ + module utilsrange +********************************************************************** +* Teste dos vínculos impostos para o cálculo VDOS * +* Flaviano Williams Fernandes, 20 de agosto de 2014 * +********************************************************************** + use sizes + use system +c + contains +c + subroutine testrange(wop,rc,ans) +c + implicit none +c + integer ans,wop,j,i + real(kind=4) rint,rend,rx,rc(iz) +c + ans=0 + rx=0. + select case(opx) + case(1) + ans=1 + case(2) + call range(wop,rint,rend) + if(rc(3).ge.rint.and.rc(3).lt.rend)ans=1 + case(3) + do j=1,atmax + if(at(j).eq.att)then + rx=0. + do i=1,iz + rx=rx+(rc(i)-r(wop,j,i))**2 + end do + rx=sqrt(rx) + if(rx.ge.rmin.and.rx.lt.rmax)ans=1 + end if + end do + end select +c + return +c + end subroutine testrange +c + subroutine range(wop,rint,rend) +c + implicit none +c + integer c,i,wop + integer ats + real(kind=4) rint,rend,az +c character*8 ats +c + ats=1 + az=-0.5*l(wop,3) + c=0 + do i=1,atmax + if(at(i).eq.ats)az=0. + end do +c + do i=1,atmax + if(at(i).eq.ats.and.r(wop,i,3).lt.0.)then + az=az+r(wop,i,3) + c=c+1 + end if + end do +c + az=az/float(max(1,c)) + rint=rmin+az + rend=rmax+az +c + return +c + end subroutine range +c + end module utilsrange diff --git a/UTILS/GRAPHS/TB-3d-grids.gnu b/UTILS/GRAPHS/TB-3d-grids.gnu new file mode 100644 index 0000000..7a0d5ed --- /dev/null +++ b/UTILS/GRAPHS/TB-3d-grids.gnu @@ -0,0 +1,87 @@ +set autoscale +reset +unset log # remove any log-scaling +unset label # remove any previous labels +set ticslevel 0.0 +set termoption enhanced +set xrange [-2.0:2.0] +set yrange [-2.0:2.0] +set term pngcairo size 600,400 font "Times-Roman,6" enhanced +#set terminal jpeg font "Times-Roman,14" +#set terminal postscript eps color "Times-Roman" 14 +#set term wxt size 600,400 "Times-Roman,12" +############################################################ +set dgrid3d 250,250 +unset hidden3d +set nokey +set contour base +set cntrparam levels incremental -22, 0.05, 6 +set pm3d map +#show palette fit2rgbformulae +set palette +#set palette defined (0. "white", 0.1 "black", 1. "black") +############################################################ +set output 'TB-3d-valencia.png' +set multiplot layout 2,2 +############################################################ +#banda 1 +col=1 +set size 0.45,0.5 +set origin 0,0.5 +set title sprintf('Band %d',col) +splot "bandas-3d.dat" u 1:2:col+3 w pm3d +# +#banda 2 +col=2 +set size 0.45,0.5 +set origin 0.5,0.5 +set title sprintf('Band %d',col) +splot "bandas-3d.dat" u 1:2:col+3 w pm3d +# +#banda 3 +col=3 +set size 0.45,0.5 +set origin 0.,0. +set title sprintf('Band %d',col) +splot "bandas-3d.dat" u 1:2:col+3 w pm3d +# +#banda 4 +col=4 +set size 0.45,0.5 +set origin 0.5,0. +set title sprintf('Band %d',col) +splot "bandas-3d.dat" u 1:2:col+3 w pm3d +############################################################ +unset multiplot +set output 'TB-3d-conducao.png' +set multiplot layout 2,2 +############################################################ +#banda 5 +col=5 +set size 0.45,0.5 +set origin 0,0.5 +set title sprintf('Band %d',col) +splot "bandas-3d.dat" u 1:2:col+3 w pm3d +# +#banda 6 +col=6 +set size 0.45,0.5 +set origin 0.5,0.5 +set title sprintf('Band %d',col) +splot "bandas-3d.dat" u 1:2:col+3 w pm3d +# +#banda 7 +col=7 +set size 0.45,0.5 +set origin 0.,0. +set title sprintf('Band %d',col) +splot "bandas-3d.dat" u 1:2:col+3 w pm3d +# +#banda 8 +col=8 +set size 0.45,0.5 +set origin 0.5,0. +set title sprintf('Band %d',col) +splot "bandas-3d.dat" u 1:2:col+3 w pm3d +############################################################ +unset multiplot diff --git a/UTILS/GRAPHS/TB-3d.gnu b/UTILS/GRAPHS/TB-3d.gnu new file mode 100644 index 0000000..aa25a72 --- /dev/null +++ b/UTILS/GRAPHS/TB-3d.gnu @@ -0,0 +1,31 @@ +set autoscale +reset +unset log # remove any log-scaling +unset label # remove any previous labels +set ticslevel 0.0 +set termoption enhanced +set xrange [-2.0:2.0] +set yrange [-2.0:2.0] +#set zrange [-2:2] +set ztics 1.0 +set xlabel "k_{x}" +set ylabel "k_{y}" +set zlabel "E(k)" +set term pngcairo size 600,400 font "Times-Roman,10" enhanced +#set terminal jpeg font "Times-Roman,14" +#set terminal postscript eps color "Times-Roman" 14 +#set term wxt size 600,400 "Times-Roman,12" +set dgrid3d 250,250 +set hidden3d +#set view 90,0 +set nokey +set contour base +set cntrparam levels incremental -22, 0.05, 6 +#set pm3d map +#show palette fit2rgbformulae +set palette +#set palette defined (0. "white", 0.1 "black", 1. "black") +do for [col=4:4] { + set title sprintf('Band %d',col) + set output sprintf('bandas-3d%d.png',col) + splot "bandas-3d.dat" u 1:2:col+3 w pm3d} diff --git a/UTILS/GRAPHS/band-graphene.gnu b/UTILS/GRAPHS/band-graphene.gnu new file mode 100644 index 0000000..12bd12f --- /dev/null +++ b/UTILS/GRAPHS/band-graphene.gnu @@ -0,0 +1,34 @@ +reset +################################################################### +#Gerando output +################################################################### +set termoption enhanced +set encoding utf8 +set term pngcairo size 600,400 font "Times-Roman,10" enhanced +#set term wxt size 600,400 "Times-Roman,12" +#set term post eps solid size 6,4 font "Times-Roman,20" enhanced +set output "TB.png" +################################################################### +#Parametros gerais!!! +################################################################### +set style arrow 1 lc rgb "black" lt 0 lw 5.0 nohead +set style line 1 lc rgb "red" lt 1 lw 1.0 +set style line 2 lc rgb "black" pt 4 ps 0.5 +set style line 3 lc rgb "red" lt 2 lw 1.5 ps 1.5 dashtype 1 +#################################################################### +#grafico estrutura de bandas +#################################################################### +# +set xrange [0.0:2.2] +set yrange [-20.0:20.0] +#set xlabel "k" +set ylabel "Energy (eV)" +set ytics 4.0 +set grid xtics ls 1 +set xtics ("K" 0.0, '{/Symbol \107}' 0.90, "M" 1.68, "K" 2.13) +#set arrow from 0.0 to 2.2 arrowstyle 1 +#set title 'Grafeno' +# +plot for [col=2:10] "TB.dat" u 1:col w l ls 1 notitle, \ + for [col=2:8] "bandas.dat" every 5 u 1:col w p ls 2 notitle +#################################################################### diff --git a/UTILS/GRAPHS/band_siesta b/UTILS/GRAPHS/band_siesta new file mode 100644 index 0000000..74d4094 Binary files /dev/null and b/UTILS/GRAPHS/band_siesta differ diff --git a/UTILS/GRAPHS/density-press.gnu b/UTILS/GRAPHS/density-press.gnu new file mode 100644 index 0000000..4be7c14 --- /dev/null +++ b/UTILS/GRAPHS/density-press.gnu @@ -0,0 +1,77 @@ +reset +set termoption enhanced +set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo solid size 6,4 font "Roman,12" +set term pngcairo size 600,900 font "Times-Roman,10" +#set term wxt size 600,400 "Times-Roman,12" +set output "densidade-press.png" +set style line 1 lc rgb "black" lt 1 lw 1 pt 7 ps 1.2 +set style line 2 lc rgb "red" lt 7 lw 1 +##################################################### +set xrange [50:1200] +set xtics 100 +set yrange [10:1200] +set ytics 150 +set ylabel 'Densidade (kg/m^3)' +unset xlabel +set multiplot layout 4,1 +set origin 0,0.75 +set bmargin 0 +set tmargin 1 +set label 'r_c = 10 A' at graph 0.05,0.75 +set label '373 K' at graph 0.85,0.7 +set label '298 K' at graph 0.85,0.82 +set label '273 K' at graph 0.85,0.9 +unset xlabel +set format x "" +plot "densidade-273K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-298K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-373K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-273K-10A.dat" u 1:2:3 w yerrorbars ls 2 notitle,\ + "densidade-298K-10A.dat" u 1:2:3 w yerrorbars ls 2 notitle,\ + "densidade-373K-10A.dat" u 1:2:3 w yerrorbars ls 2 notitle +set origin 0,0.5 +set bmargin 0 +set tmargin 0 +unset label +set label 'r_c = 8 A' at graph 0.05,0.75 +set label '373 K' at graph 0.85,0.7 +set label '298 K' at graph 0.85,0.82 +set label '273 K' at graph 0.85,0.9 +plot "densidade-273K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-298K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-373K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-273K-8A.dat" u 1:2:3 w yerrorbars ls 2 notitle,\ + "densidade-298K-8A.dat" u 1:2:3 w yerrorbars ls 2 notitle,\ + "densidade-373K-8A.dat" u 1:2:3 w yerrorbars ls 2 notitle +set origin 0,0.25 +#set bmargin 1 +#set tmargin 0 +unset label +set label 'r_c = 6 A' at graph 0.05,0.75 +set label '373 K' at graph 0.85,0.7 +set label '298 K' at graph 0.85,0.82 +set label '273 K' at graph 0.85,0.9 +plot "densidade-273K-exp.dat" u 1:2 w lp ls 1 notitle, \ + "densidade-298K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-373K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-273K-6A.dat" u 1:2:3 w yerrorbars ls 2 notitle,\ + "densidade-298K-6A.dat" u 1:2:3 w yerrorbars ls 2 notitle,\ + "densidade-373K-6A.dat" u 1:2:3 w yerrorbars ls 2 notitle +set origin 0,0.0 +#set tmargin 0 +set bmargin 3 +unset label +set label 'r_c = 4 A' at graph 0.05,0.75 +set label '373 K' at graph 0.85,0.7 +set label '298 K' at graph 0.85,0.82 +set label '273 K' at graph 0.85,0.9 +set xlabel 'Pressão (atm)' +set format x "%5.0f" +plot "densidade-273K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-298K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-373K-exp.dat" u 1:2 w lp ls 1 notitle,\ + "densidade-273K-4A.dat" u 1:2:3 w yerrorbars ls 2 notitle,\ + "densidade-298K-4A.dat" u 1:2:3 w yerrorbars ls 2 notitle +unset multiplot diff --git a/UTILS/GRAPHS/density.gnu b/UTILS/GRAPHS/density.gnu new file mode 100644 index 0000000..ab9a4ac --- /dev/null +++ b/UTILS/GRAPHS/density.gnu @@ -0,0 +1,24 @@ +reset +set termoption enhanced +set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo solid size 6,4 font "Roman,12" +#set term pngcairo size 600,400 font "Times-Roman,12" +#set term wxt size 600,400 "Times-Roman,12" +#set output "densidade.png" +#set xrange [0.5:3.5] +#set xtics 1 +set style line 1 lc rgb "black" lt 5 lw 1 +set style line 2 lc rgb "red" lt 5 lw 1 +set style line 3 lc rgb "green" lt 4 lw 1 +##################################################### +#set format x "" +set xlabel 'Temperatura (K)' +#set format y "%5.2f" +#set yrange [1.16:1.65] +#set ytics 0.1 +set ylabel 'Densidade (kg/m^3)' +set style line 1 lt 1 lw 1 pt 7 ps 1.2 +plot "densidade-exp.dat" u 1:2 w lp ls 1 title "Experimental", \ + "densidade-mod1.dat" u 1:2 w lp ls 2 title "Simulado", \ + "densidade-mod2.dat" u 1:2 w lp ls 3 title "Simulado" diff --git a/UTILS/GRAPHS/dipole.gnu b/UTILS/GRAPHS/dipole.gnu new file mode 100644 index 0000000..4c053ab --- /dev/null +++ b/UTILS/GRAPHS/dipole.gnu @@ -0,0 +1,23 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +#set term pngcairo size 600,400 font "Times-Roman,10" enhanced +#set output "dipole.png" +set style arrow 1 lc rgb "red" lt 1 lw 1 nohead +set style line 1 lc rgb "black" lt 7 lw 0.25 +set style line 2 lc rgb "black" lt 5 lw 1 +#set xrange [300:400] +set xlabel "Dipole (D)" +#set yrange [0:1000] +set ylabel "Probability" +set key off + +stats 'probability.dat' using 2:3 name "A" +stats 'probability.dat' using 3 name "B" +#set label 1 gprintf("Mean = %g", mean_y) at 2,0.35 +set arrow 2 from A_pos_max_y,0 to A_pos_max_y,B_max arrowstyle 1 front + +plot 'probability.dat' u 8:9 w l ls 1 title "Dipolo", \ + 'probability.dat' u 8:9 ls 2 smooth bezier notitle diff --git a/UTILS/GRAPHS/dsv-tstat.gnu b/UTILS/GRAPHS/dsv-tstat.gnu new file mode 100644 index 0000000..2e20a12 --- /dev/null +++ b/UTILS/GRAPHS/dsv-tstat.gnu @@ -0,0 +1,18 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo solid size 6,4 font "Roman,12" +#set term pngcairo enhanced size 600,400 font "Times-Roman,10" +#set output "dsv-tstat.png" +#set xrange [0:0.6] +#set xtics 1 +##################################################### +# GAP x layer +set xlabel 'tstat (ps)' +#set format y "%5.0f" +#set yrange [370:374] +#set ytics 0.1 +set ylabel 'Desvio padrão (eV)' +set style line 1 lt 1 lw 1 pt 7 ps 1.2 +plot 'dsv-tstat.dat' u 1:2 w lp ls 1 notitle diff --git a/UTILS/GRAPHS/energy-npt.gnu b/UTILS/GRAPHS/energy-npt.gnu new file mode 100644 index 0000000..2c50ffb --- /dev/null +++ b/UTILS/GRAPHS/energy-npt.gnu @@ -0,0 +1,18 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +set term pngcairo size 600,400 font "Times-Roman,10" enhanced +set output "energia-npt.png" +#set style arrow 1 lc rgb "red" lt 1 lw 1 nohead +set style line 1 lc rgb "black" lt 5 lw 1 +#set xrange [300:400] +set xlabel "Tempo (ps)" +#set yrange [0:1000] +set ylabel "Energia (eV)" +#set arrow from 0,371.43 to 100,371.43 arrowstyle 1 front +plot "energia-npt-373K.dat" u 1:2 w l ls 1 notitle, \ + "energia-npt-273K.dat" u 1:2 w l ls 1 notitle, \ + "energia-npt-173K.dat" u 1:2 w l ls 1 notitle, \ + "energia-npt-73K.dat" u 1:2 w l ls 1 notitle diff --git a/UTILS/GRAPHS/energy-nve.gnu b/UTILS/GRAPHS/energy-nve.gnu new file mode 100644 index 0000000..1b67474 --- /dev/null +++ b/UTILS/GRAPHS/energy-nve.gnu @@ -0,0 +1,15 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +#set term pngcairo size 600,400 font "Times-Roman,10" enhanced +#set output "energia.png" +#set style arrow 1 lc rgb "red" lt 1 lw 1 nohead +set style line 1 lc rgb "black" lt 5 lw 1 +#set xrange [300:400] +set xlabel "Tempo (ps)" +#set yrange [0:1000] +set ylabel "Energia (eV)" +#set arrow from 0,371.43 to 100,371.43 arrowstyle 1 front +plot "energia-nve.dat" u 1:2 w l ls 1 notitle diff --git a/UTILS/GRAPHS/energy-nvt.gnu b/UTILS/GRAPHS/energy-nvt.gnu new file mode 100644 index 0000000..0f0f979 --- /dev/null +++ b/UTILS/GRAPHS/energy-nvt.gnu @@ -0,0 +1,18 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +#set term pngcairo size 600,400 font "Times-Roman,10" enhanced +#set output "energia-nvt.png" +#set style arrow 1 lc rgb "red" lt 1 lw 1 nohead +set style line 1 lc rgb "black" lt 5 lw 1 +#set xrange [300:400] +set xlabel "Tempo (ps)" +#set yrange [0:1000] +set ylabel "Energia (eV)" +#set arrow from 0,371.43 to 100,371.43 arrowstyle 1 front +plot "energia-nvt-373K.dat" u 1:2 w l ls 1 notitle, \ + "energia-nvt-273K.dat" u 1:2 w l ls 1 notitle, \ + "energia-nvt-173K.dat" u 1:2 w l ls 1 notitle, \ + "energia-nvt-73K.dat" u 1:2 w l ls 1 notitle diff --git a/UTILS/GRAPHS/gap.gnu b/UTILS/GRAPHS/gap.gnu new file mode 100644 index 0000000..11b18cf --- /dev/null +++ b/UTILS/GRAPHS/gap.gnu @@ -0,0 +1,50 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo solid size 6,4 font "Roman,12" +set term png size 600,400 font "Times-Roman,12" +#set term wxt size 600,400 "Times-Roman,12" +set output "gap.png" +set multiplot layout 2,1 +set xrange [0.5:3.5] +set xtics 1 +set size 1,0.5 +##################################################### +# GAP x layer +set origin 0,0.5 +unset xlabel +set format x "" +#set xlabel 'Graphene layer' +set bmargin 0 +set format y "%5.2f" +set yrange [1.16:1.65] +set ytics 0.1 +set ylabel 'Energy (eV)' +set style line 1 lt 1 lw 1 pt 7 ps 1.2 +set key title 'GAP' +plot '-' u 1:2 w lp ls 1 notitle +1 1.61 +2 1.34 +3 1.22 +e +##################################################### +# Ebind x layer +unset format +unset bmargin +set tmargin 0 +set origin 0,0 +set yrange [-8.25:-8.05] +set ytics 0.04 +set xlabel 'Graphene layer' +set format y "%5.2f" +set ylabel 'Energy (eV)' +set style line 1 lt 1 lw 1 pt 7 ps 1.2 +set key title 'Binding energy' +plot '-' u 1:2 w lp ls 1 notitle +1 -8.06 +2 -8.20 +3 -8.23 +e +##################################################### +unset multiplot diff --git a/UTILS/GRAPHS/infrared.gnu b/UTILS/GRAPHS/infrared.gnu new file mode 100644 index 0000000..ce70a3e --- /dev/null +++ b/UTILS/GRAPHS/infrared.gnu @@ -0,0 +1,62 @@ +reset +set termoption enhanced +set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +set term pngcairo size 600,400 font "Times-Roman,10" enhanced +set output "infrared.png" +set style arrow 1 lc rgb "gray" lw 1 dt 3 nohead +set style arrow 2 lc rgb "black" lw 1 dt 1 filled size screen 0.02,15,45 +set style line 1 lw 1 lc rgb "black" dt 1 +set style line 2 lw 1 lc rgb "red" dt 1 +set style line 3 lw 1 lc rgb "green" dt 1 +######################################################################## +set multiplot +######################################################################## +#plot 1 +######################################################################## +set origin 0,0 +set xrange [0:4000] +set xlabel "Frequency (cm^{-1})" +set yrange [0:0.08] +set ylabel "Intensity" +unset ytics +set key on at 3100,0.03 +set arrow from 3610,0 to 3610,0.08 arrowstyle 1 front +set arrow from 3733,0 to 3733,0.08 arrowstyle 1 front +set arrow from 1455,0 to 1455,0.08 arrowstyle 1 front +set arrow from 1525,0 to 1525,0.08 arrowstyle 1 front + +set arrow from 1525,0.048 to 1525,0.04 arrowstyle 2 front +set label "1525" left at 1525,0.048 font "Times-Roman,8" offset 0.1,0.5 +set arrow from 1455,0.058 to 1455,0.05 arrowstyle 2 front +set label "1455" center at 1455,0.058 font "Times-Roman,8" offset 0.1,0.5 +set arrow from 3733,0.064 to 3733,0.056 arrowstyle 2 front +set label "3733" center at 3733,0.064 font "Times-Roman,8" offset 0.1,0.5 +set arrow from 3610,0.069 to 3610,0.061 arrowstyle 2 front +set label "3610" center at 3610,0.069 font "Times-Roman,8" offset 0.1,0.5 + +plot "infrared.dat" u 1:3 w l ls 1 title "stretch", \ + "infrared.dat" u 1:4 w l ls 2 title "libration", \ + "infrared.dat" u 1:5 w l ls 3 title "oxygen", \ + "infrared.dat" u 1:6 w l ls 4 title "hydrogen" +######################################################################## +#plot 1 +######################################################################## +set origin 0.5,0.55 +set size 0.35,0.35 +set key off +unset label +unset arrow +unset xlabel +unset ylabel +unset xrange +set yrange [-1:1] +set xtics 0.2 +set ytics 1 +plot "vacf.dat" u 1:3 w l ls 1 notitle, \ + "vacf.dat" u 1:4 w l ls 2 notitle, \ + "vacf.dat" u 1:5 w l ls 3 notitle, \ + "vacf.dat" u 1:6 w l ls 4 notitle +######################################################################## +unset multiplot diff --git a/UTILS/GRAPHS/pdos-1layer.gnu b/UTILS/GRAPHS/pdos-1layer.gnu new file mode 100644 index 0000000..7bf7f70 --- /dev/null +++ b/UTILS/GRAPHS/pdos-1layer.gnu @@ -0,0 +1,79 @@ +reset +set termoption enhanced +#set encoding utf8 +set term post eps solid size 6,8 font "Times-Roman,20" +set output "pdos-1layer.eps" +#set term png size 600,400 font "Times-Roman,14" enhanced +#set term wxt size 600,800 "Times-Roman,12" +set style arrow 1 lt 0 lw 4 nohead +set style line 2 lc rgb "black" lt 1 lw 4 +set style line 3 lc rgb "red" lt 1 lw 4 +set style line 4 lc rgb "green" lt 1 lw 4 +set xrange [-4:4] +set ylabel "PDOS" +set mytics 2 +################################################################### +set multiplot layout 2,1 +# +#configurando grafico PDOS do zinco +# +set format x "" +set yrange [0:1000] +set bmargin 0 +set size 1,0.25 +set origin 0,0.75 +set arrow from 0,0 to 0,1000 arrowstyle 1 +plot "PDOS-Zn1-1layer.dat" u ($1*27+3.07827):2 w l ls 2 title "Zn_{s}", \ + "PDOS-Zn1-1layer.dat" u ($1*27+3.07827):3 w l ls 3 title "Zn_{p}", \ + "PDOS-Zn1-1layer.dat" u ($1*27+3.07827):4 w l ls 4 title "Zn_{d}" +# +unset format +unset bmargin +unset yrange +unset arrow +# +set xlabel "E-E_{F} (eV)" +set yrange [1000:0] +set tmargin 0 +set size 1,0.25 +set origin 0,0.50 +set arrow from 0,0 to 0,1000 arrowstyle 1 +plot "zno_xo_DS2_DOS_AT0001" u ($1*27-2.9832):2 w l ls 2 notitle, \ + "zno_xo_DS2_DOS_AT0001" u ($1*27-2.9832):3 w l ls 3 notitle, \ + "zno_xo_DS2_DOS_AT0001" u ($1*27-2.9832):4 w l ls 4 notitle +# +unset tmargin +unset arrow +unset yrange +unset xlabel +##################################################################### +#configurando grafico PDOS do oxigenio +# +set format x "" +set yrange [0:2500] +set bmargin 0 +set size 1,0.25 +set origin 0,0.25 +set arrow from 0,0 to 0,2500 arrowstyle 1 +plot "PDOS-O1-1layer.dat" u ($1*27+3.07827):2 w l ls 2 title "Zn_{s}", \ + "PDOS-O1-1layer.dat" u ($1*27+3.07827):3 w l ls 3 title "Zn_{p}", \ + "PDOS-O1-1layer.dat" u ($1*27+3.07827):4 w l ls 4 title "Zn_{d}" +# +unset format +unset bmargin +unset yrange +unset xlabel +unset arrow +# +set xlabel "E-E_{F} (eV)" +set yrange [2500:0] +set tmargin 0 +set size 1,0.25 +set origin 0,0.0 +set arrow from 0,0 to 0,2500 arrowstyle 1 +plot "zno_xo_DS2_DOS_AT0003" u ($1*27-2.9832):2 w l ls 2 notitle, \ + "zno_xo_DS2_DOS_AT0003" u ($1*27-2.9832):3 w l ls 3 notitle, \ + "zno_xo_DS2_DOS_AT0003" u ($1*27-2.9832):4 w l ls 4 notitle +# +unset multiplot +##################################################################### \ No newline at end of file diff --git a/UTILS/GRAPHS/pressure.gnu b/UTILS/GRAPHS/pressure.gnu new file mode 100644 index 0000000..8954a6a --- /dev/null +++ b/UTILS/GRAPHS/pressure.gnu @@ -0,0 +1,15 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +set term pngcairo size 600,400 font "Times-Roman,10" enhanced +set output "pressao.png" +#set style arrow 1 lc rgb "red" lt 1 lw 1 nohead +set style line 2 lc rgb "black" lt 1 lw 1 +#set xrange [300:400] +set xlabel "Tempo (ps)" +#set yrange [0:1000] +set ylabel "Temperatura (K)" +#set arrow from 0,371.43 to 100,371.43 arrowstyle 1 front +plot "temperatura-4.dat" u 1:2 w l ls 2 notitle diff --git a/UTILS/GRAPHS/pstat.gnu b/UTILS/GRAPHS/pstat.gnu new file mode 100644 index 0000000..440bc54 --- /dev/null +++ b/UTILS/GRAPHS/pstat.gnu @@ -0,0 +1,35 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo solid size 6,4 font "Roman,12" +#set term pngcairo enhanced size 600,400 font "Times-Roman,10" +#set output "tstat.png" +set style line 1 lc "black" lt 1 lw 1 pt 7 ps 1.2 +set style line 2 lc "black" lt 1 lw 1 pt 7 ps 1.2 +set multiplot +##################################################### +# desvio padrao da energia +set xrange [0.0005:1] +set origin 0,0 +set size 1,1 +set xlabel 'pstat (ps)' +set logscale x +#set xtics 0.01 +#set format y "%5.0f" +#set yrange [370:374] +#set ytics 0.1 +set ylabel 'Flutuação na energia total (eV)' +plot 'pstat.dat' u 1:2 w lp ls 1 notitle,\ + 'pstat.dat' u 1:2 smooth cspline notitle +##################################################### +# temperatura media +unset xlabel +set origin 0.2,0.5 +set size 0.4,0.4 +set format y "%5.0f" +set yrange [4:10] +set ytics 1 +set ylabel '{/Symbol D}T (K)' offset 3,0 +plot 'pstat.dat' u 1:3 w lp ls 2 notitle +unset multiplot diff --git a/UTILS/GRAPHS/rcutoff.gnu b/UTILS/GRAPHS/rcutoff.gnu new file mode 100644 index 0000000..0620a32 --- /dev/null +++ b/UTILS/GRAPHS/rcutoff.gnu @@ -0,0 +1,41 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo solid size 6,4 font "Roman,12" +set term pngcairo enhanced size 600,400 font "Times-Roman,10" +set output "rcutoff.png" +set multiplot layout 2,1 +set xrange [4:10] +set xtics 0.5 +set size 1,0.5 +set style line 1 lc "black" lt 1 lw 1 pt 7 ps 1.2 +##################################################### +# GAP x layer +set origin 0,0.5 +unset xlabel +set format x "" +#set xlabel 'Graphene layer' +set bmargin 0 +set format y "%5.0f" +set yrange [70:250] +set ytics 50 +set ylabel 'Tempo (s)' +set label 'Tempo de CPU' center at graph 0.8,0.2 +plot "rcutoff.dat" u 1:2 w lp ls 1 notitle +##################################################### +# Ebind x layer +unset format +unset bmargin +unset label +set tmargin 0 +set origin 0,0 +set yrange [-2:0] +set ytics 0.5 +set xlabel 'r_c (A)' +set format y "%5.1f" +set ylabel 'Energia (eV)' +set label 'Correção de VdW' center at graph 0.8,0.2 +plot "rcutoff.dat" u 1:3 w lp ls 1 notitle +##################################################### +unset multiplot diff --git a/UTILS/GRAPHS/rcutoff2.gnu b/UTILS/GRAPHS/rcutoff2.gnu new file mode 100644 index 0000000..70697f7 --- /dev/null +++ b/UTILS/GRAPHS/rcutoff2.gnu @@ -0,0 +1,40 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo solid size 6,4 font "Roman,12" +set term pngcairo enhanced size 600,400 font "Times-Roman,10" +set output "rcutoff.png" +set multiplot layout 2,1 +#set xrange [0.5:3.5] +set xtics 0.5 +set size 1,0.5 +set style line 1 lc "black" lt 1 lw 1 pt 7 ps 1.2 +##################################################### +# GAP x layer +set origin 0,0.5 +unset xlabel +set format x "" +#set xlabel 'Graphene layer' +set bmargin 0 +set format y "%5.2f" +#set yrange [1.16:1.65] +#set ytics 0.1 +set ylabel 'Tempo (s)' +set key title 'Tempo de CPU' +plot "rcutoff.dat" u 1:2 w lp ls 1 notitle +##################################################### +# Ebind x layer +unset format +unset bmargin +set tmargin 0 +set origin 0,0 +#set yrange [-8.25:-8.05] +#set ytics 0.04 +set xlabel 'r_c (A)' +set format y "%5.2f" +set ylabel 'Energia (eV)' +set key title 'Correção de VdW' +plot "rcutoff.dat" u 1:3 w lp ls 1 notitle +##################################################### +unset multiplot diff --git a/UTILS/GRAPHS/rdf-130K.gnu b/UTILS/GRAPHS/rdf-130K.gnu new file mode 100644 index 0000000..be8c66a --- /dev/null +++ b/UTILS/GRAPHS/rdf-130K.gnu @@ -0,0 +1,17 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +#set term pngcairo size 600,400 font "Times-Roman,10" enhanced +#set output "rcutoff.png" +#set style arrow 1 lc rgb "red" lt 1 lw 1 nohead +set style line 1 lc rgb "black" lt 7 lw 0.25 +set style line 2 lc rgb "black" lt 5 lw 1 +#set xrange [300:400] +set xlabel "r (A)" +#set yrange [0:1000] +set ylabel "RDF" +#set arrow from 0,371.43 to 100,371.43 arrowstyle 1 front +plot "rdf-Ar-exp-130K.dat" u 1:2 w p ls 1 title "Experimental", \ + "rdf-simulado-130K.dat" u 1:2 w l ls 2 title "Calculado" diff --git a/UTILS/GRAPHS/rdf-92K.gnu b/UTILS/GRAPHS/rdf-92K.gnu new file mode 100644 index 0000000..f33cb90 --- /dev/null +++ b/UTILS/GRAPHS/rdf-92K.gnu @@ -0,0 +1,17 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +set term pngcairo size 600,400 font "Times-Roman,10" enhanced +set output "rdf-92K.png" +#set style arrow 1 lc rgb "red" lt 1 lw 1 nohead +set style line 1 lc rgb "black" lt 7 lw 0.25 +set style line 2 lc rgb "black" lt 5 lw 1.5 +#set xrange [300:400] +set xlabel "r (A)" +#set yrange [0:1000] +set ylabel "RDF" +#set arrow from 0,371.43 to 100,371.43 arrowstyle 1 front +plot "rdf-Ar-exp.dat" u 1:2 w p ls 1 title "Experimental", \ + "rdf-simulado-92K.dat" u 1:2 w l ls 2 title "Calculado" diff --git a/UTILS/GRAPHS/temperature.gnu b/UTILS/GRAPHS/temperature.gnu new file mode 100644 index 0000000..1509944 --- /dev/null +++ b/UTILS/GRAPHS/temperature.gnu @@ -0,0 +1,15 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +#set term pngcairo size 600,400 font "Times-Roman,10" enhanced +#set output "temperatura.png" +#set style arrow 1 lc rgb "red" lt 1 lw 1 nohead +set style line 1 lc rgb "black" lt 1 lw 1 +#set xrange [300:400] +set xlabel "Tempo (ps)" +#set yrange [0:1000] +set ylabel "Temperatura (K)" +#set arrow from 0,371.43 to 100,371.43 arrowstyle 1 front +plot "TBMD.dat" u 7:9 w l ls 1 notitle diff --git a/UTILS/GRAPHS/tstat.gnu b/UTILS/GRAPHS/tstat.gnu new file mode 100644 index 0000000..e198196 --- /dev/null +++ b/UTILS/GRAPHS/tstat.gnu @@ -0,0 +1,35 @@ +reset +set termoption enhanced +#set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo solid size 6,4 font "Roman,12" +set term pngcairo enhanced size 600,400 font "Times-Roman,10" +set output "tstat.png" +set style line 1 lc "black" lt 1 lw 1 pt 7 ps 1.0 +set style line 2 lc "black" lt 1 lw 1 pt 7 ps 1.0 +set multiplot +##################################################### +# desvio padrao da energia +set xrange [0.0005:1] +set origin 0,0 +set size 1,1 +set xlabel '{/Symbol t}_T (ps)' +set logscale x 10 +set format y "%5.2f" +set yrange [0.05:0.35] +#set ytics 0.1 +set samples 1000 +set ylabel 'Flutuação na energia total (eV)' +plot 'tstat.dat' u 1:2 w p ls 1 notitle,\ + 'tstat.dat' u 1:2 smooth sbezier ls 1 notitle +##################################################### +# temperatura media +unset xlabel +set origin 0.5,0.55 +set size 0.4,0.4 +set format y "%5.0f" +set yrange [0:15] +set ytics 3 +set ylabel '{/Symbol D}T (K)' offset 3,0 +plot 'tstat.dat' u 1:3 w lp ls 2 notitle +unset multiplot diff --git a/UTILS/GRAPHS/vacf.gnu b/UTILS/GRAPHS/vacf.gnu new file mode 100644 index 0000000..d19c61a --- /dev/null +++ b/UTILS/GRAPHS/vacf.gnu @@ -0,0 +1,19 @@ +reset +set termoption enhanced +set encoding utf8 +#set term post eps solid size 6,4 font "Times-Roman,20" +#set term pdfcairo enhanced size 600,400 font "Times-Roman,14" +#set term pngcairo size 600,400 font "Times-Roman,10" enhanced +#set output "vacf.png" +set style line 1 lw 1 lc rgb "black" dt 1 +set style line 2 lw 1 lc rgb "red" dt 1 +set style line 3 lw 1 lc rgb "green" dt 1 +#set xrange [0:0.1] +set xlabel "Time (ps)" +#set yrange [0:1000] +set ylabel "VACF" +plot "vacf.dat" u 1:2 w l ls 1 title "stretch", \ + "vacf.dat" u 1:3 w l ls 2 title "stretch", \ + "vacf.dat" u 1:4 w l ls 3 title "libration", \ + "vacf.dat" u 1:5 w l ls 3 title "1", \ + "vacf.dat" u 1:6 w l ls 3 title "2" diff --git a/UTILS/SCRIPTS/densidade-pressao.sh b/UTILS/SCRIPTS/densidade-pressao.sh new file mode 100644 index 0000000..1b9f932 --- /dev/null +++ b/UTILS/SCRIPTS/densidade-pressao.sh @@ -0,0 +1,21 @@ +#!/bin/bash +# Limpando arquivos +rm densidade-press.dat +# Atribuindo valores iniciais +aini=100 +afin=1000 +passo=100 +a=$aini +while [ $(echo "$a<=$afin"|bc) -eq 1 ];do +# Alterando input +sed -i -e "s/.*preext.*/preext $a/" TBMD.in +# Rodando TBMC +./TBMD +./tbmc +d=$(awk '/MED2/ {print $3}' TBMD.dat) +ds=$(awk '/DSV2/ {print $3}' TBMD.dat) +# Imprimindo em arquivo dat +echo $a $d $ds >> densidade-press.dat +# Atribuindo valores +a=$(echo "$a+$passo"|bc) +done diff --git a/UTILS/SCRIPTS/densidade.sh b/UTILS/SCRIPTS/densidade.sh new file mode 100644 index 0000000..f4f2b28 --- /dev/null +++ b/UTILS/SCRIPTS/densidade.sh @@ -0,0 +1,19 @@ +#!/bin/bash +# Limpando arquivos +rm densidade.dat +# Atribuindo valores iniciais +aini=73 +afin=373 +passo=25 +a=$aini +while [ $(echo "$a<=$afin"|bc) -eq 1 ];do +# Alterando input +sed -i -e "s/.*text.*/text $a/" TBMC.in +# Rodando TBMC +./TBMC +d=$(awk '/DENSIDADE/ {print $2}' TBMC.out) +# Imprimindo em arquivo dat +echo $a $d >> densidade.dat +# Atribuindo valores +a=$(echo "$a+$passo"|bc) +done diff --git a/UTILS/SCRIPTS/drmax.sh b/UTILS/SCRIPTS/drmax.sh new file mode 100644 index 0000000..993f8c1 --- /dev/null +++ b/UTILS/SCRIPTS/drmax.sh @@ -0,0 +1,21 @@ +#!/bin/bash +# Limpando arquivos +rm drmax.dat +# Atribuindo valores iniciais +aini=0.1 +afin=0.01 +passo=-0.001 +a=$aini +while [ $(echo "$a>=$afin"|bc) -eq 1 ];do +# Alterando input +sed -i -e "s/.*drmax.*/drmax $a/" TBMC.in +# Rodando TBMC +./TBMC +es=$(awk '/simula.:/ {print $3}' TBMC.out) +E=$(awk '/TOTL):/ {print $2}' TBMC.out) +dE=$(awk '/TOTL):/ {print $3}' TBMC.out) +# Imprimindo em arquivo dat +echo $a $es $E $dE >> drmax.dat +# Atribuindo valores +a=$(echo "$a+$passo"|bc) +done diff --git a/UTILS/SCRIPTS/encode.sh b/UTILS/SCRIPTS/encode.sh new file mode 100644 index 0000000..d3c2c0b --- /dev/null +++ b/UTILS/SCRIPTS/encode.sh @@ -0,0 +1,9 @@ + +# ------------------------------------------------------------------------ +# You may edit the movie encoder command below (don't touch this comment) +# ------------------------------------------------------------------------ + +/usr/bin/convert /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0000.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0001.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0002.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0003.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0004.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0005.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0006.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0007.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0008.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0009.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0010.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0011.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0012.png 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/home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0193.png /home/flaviano/Dropbox/codigos/IFPR/TBMD/anim-0194.png -set delay 10 -loop 0 /home/flaviano/Dropbox/codigos/IFPR/TBMD/teste.gif + + + diff --git a/UTILS/SCRIPTS/lrmax.sh b/UTILS/SCRIPTS/lrmax.sh new file mode 100644 index 0000000..195b7d6 --- /dev/null +++ b/UTILS/SCRIPTS/lrmax.sh @@ -0,0 +1,24 @@ +#!/bin/bash +# Limpando arquivos +rm lrmax.dat lrmax-*.out +# Atribuindo valores iniciais +aini=0.001 +afin=0.0001 +passo=-0.00005 +a=$aini +while [ $(echo "$a>=$afin"|bc) -eq 1 ];do +# Alterando input +sed -i -e "s/.*lrmax.*/lrmax $a 2/" TBMC.in +# Rodando TBMC +./TBMC +es=$(awk '/simula.:/ {print $3}' TBMC.out) +E=$(awk '/TOTL):/ {print $2}' TBMC.out) +dE=$(awk '/TOTL):/ {print $3}' TBMC.out) +v=$(awk '/F):/ {print $2}' TBMC.out) +dv=$(awk '/F):/ {print $3}' TBMC.out) +cp TBMC.out lrmax-$a.out +# Imprimindo em arquivo dat +echo $a $es $v $dv $E $dE >> lrmax.dat +# Atribuindo valores +a=$(echo "$a+$passo"|bc) +done diff --git a/UTILS/SCRIPTS/ntrialmax.sh b/UTILS/SCRIPTS/ntrialmax.sh new file mode 100644 index 0000000..5fa8ded --- /dev/null +++ b/UTILS/SCRIPTS/ntrialmax.sh @@ -0,0 +1,24 @@ +#!/bin/bash +# Limpando arquivos +rm ntrialmax.dat ntrialmax-*.out +# Atribuindo valores iniciais +aini=10000 +afin=100000 +passo=10000 +a=$aini +while [ $(echo "$a<=$afin"|bc) -eq 1 ];do +# Alterando input +sed -i -e "s/.*ntrialmax.*/ntrialmax $a/" TBMC.in +# Rodando TBMC +./TBMC +es=$(awk '/simula.:/ {print $3}' TBMC.out) +E=$(awk '/TOTL):/ {print $2}' TBMC.out) +dE=$(awk '/TOTL):/ {print $3}' TBMC.out) +v=$(awk '/F):/ {print $2}' TBMC.out) +dv=$(awk '/F):/ {print $3}' TBMC.out) +cp TBMC.out ntrialmax-$a.out +# Imprimindo em arquivo dat +echo $a $es $v $dv $E $dE >> ntrialmax.dat +# Atribuindo valores +a=$(echo "$a+$passo"|bc) +done diff --git a/UTILS/SCRIPTS/pstat.sh b/UTILS/SCRIPTS/pstat.sh new file mode 100644 index 0000000..88f3a49 --- /dev/null +++ b/UTILS/SCRIPTS/pstat.sh @@ -0,0 +1,21 @@ +#!/bin/bash +# Limpando arquivos +rm *.md +# Atribuindo valores iniciais +aini=0.05 +afin=0.005 +passo=-0.005 +a=$aini +while [ $(echo "$a>=$afin"|bc) -eq 1 ];do +# Alterando input +sed -i -e "s/.*ensemble.*/ensemble npt $a 0.1 4.9d-5/" TBMC.in +# Rodando TBMC +./TBMC +./TBMC2 +t=$(awk '/DSV1/ {print $5}' TBMC.dat) +de=$(awk '/DSV1/ {print $8}' TBMC.dat) +#imprimindo em arquivo dat +echo $a $de $t >> pstat.dat +# Atribuindo valores +a=$(echo "$a+$passo"|bc) +done diff --git a/UTILS/SCRIPTS/rcutoff.sh b/UTILS/SCRIPTS/rcutoff.sh new file mode 100644 index 0000000..09ee87e --- /dev/null +++ b/UTILS/SCRIPTS/rcutoff.sh @@ -0,0 +1,20 @@ +#!/bin/bash +# Limpando arquivos +rm rcutoff.dat +# Atribuindo valores iniciais +aini=4 +afin=10 +passo=0.5 +a=$aini +while [ $(echo "$a<=$afin"|bc) -eq 1 ];do +# Alterando input +sed -i -e "s/.*rcutoff.*/rcutoff $a 0.1/" TBMC.in +# Rodando TBMC +./TBMC +t=$(awk '/Tempo estimado/ {print $4}' TBMC.out) +c=$(awk '/energia de vdw/ {print $6}' TBMC.out) +# Imprimindo em arquivo dat +echo $a $t $c >> rcutoff.dat +# Atribuindo valores +a=$(echo "$a+$passo"|bc) +done diff --git a/UTILS/SCRIPTS/script.sh b/UTILS/SCRIPTS/script.sh new file mode 100644 index 0000000..2c0f339 --- /dev/null +++ b/UTILS/SCRIPTS/script.sh @@ -0,0 +1,19 @@ +# Limpando arquivos +rm *.dat *.out +# Atribuindo valores iniciais +aini=1 +afin=12 +passo=1 +a=$aini +while [ $(echo "$a<=$afin"|bc) -eq 1 ];do +# Alterando input +sed -i -e "s/.*monkhorst.*/monkhorst $a $a 1/" TB.in +# Rodando siesta +./TB +E=$(awk '/Energia/ {print $3}' TB.out) +mv TB.out TB-$a.out +# Imprimindo em arquivo dat +echo $a $E >> teste.dat +# Atribuindo valores +a=$(echo "$a+$passo"|bc) +done diff --git a/UTILS/SCRIPTS/tstat.sh b/UTILS/SCRIPTS/tstat.sh new file mode 100644 index 0000000..1b267bc --- /dev/null +++ b/UTILS/SCRIPTS/tstat.sh @@ -0,0 +1,21 @@ +#!/bin/bash +# Limpando arquivos +rm *.md TBMC.dat +# Atribuindo valores iniciais +aini=0.01 +afin=0.001 +passo=-0.001 +a=$aini +while [ $(echo "$a>=$afin"|bc) -eq 1 ];do +# Alterando input +sed -i -e "s/.*ensemble.*/ensemble npt $a 0.1 4.9d-5/" TBMC.in +# Rodando TBMC +./TBMC +./TBMC2 +t=$(awk '/DSV1/ {print $5}' TBMC.dat) +de=$(awk '/DSV1/ {print $8}' TBMC.dat) +#imprimindo em arquivo dat +echo $a $de $t >> tstat.dat +# Atribuindo valores +a=$(echo "$a+$passo"|bc) +done diff --git a/UTILS/proprierties.f90 b/UTILS/proprierties.f90 new file mode 100644 index 0000000..c1623c8 --- /dev/null +++ b/UTILS/proprierties.f90 @@ -0,0 +1,306 @@ +module variaveis_module + + implicit none + +contains + + subroutine variaveis(nstp,nat) + + implicit none + + integer i,j,k,nstp,nat,varmax + + parameter (varmax=13) + + real(8) var(varmax),sum(varmax),med(varmax),dsv(varmax) + + do i=1,varmax + sum(i)=0.d0 + end do + + do i=1,nstp + read(1,*) + read(1,*)(var(j),j=1,6) + read(1,*)(var(j),j=7,12) + read(1,*)(var(j),j=13,varmax) + do k=1,5 + read(1,*) + end do + do k=1,nat + read(1,*) + read(1,*) + read(1,*) + end do + do j=1,varmax + sum(j)=sum(j)+var(j) + end do + write(2,'(13f12.4)')(var(j),j=1,13) + end do + + do j=1,varmax + med(j)=sum(j)/nstp + end do + + rewind(1) + + read(1,*) + + do j=1,varmax + sum(j)=0.d0 + end do + + do i=1,nstp + read(1,*) + read(1,*)(var(j),j=1,6) + read(1,*)(var(j),j=7,12) + read(1,*)(var(j),j=13,varmax) + do k=1,5 + read(1,*) + end do + do k=1,nat + read(1,*) + read(1,*) + read(1,*) + end do + do j=1,varmax + sum(j)=sum(j)+(var(j)-med(j))**2 + end do + end do + + do j=1,varmax + dsv(j)=sqrt(sum(j)/(nstp-1)) + end do + + write(2,*) + write(2,*)'# MED1',(med(i),i=1,6) + write(2,*)'# DSV1',(dsv(i),i=1,6) + write(2,*) + write(2,*)'# MED2',(med(i),i=7,12) + write(2,*)'# DSV2',(dsv(i),i=7,12) + write(2,*) + write(2,*)'# MED3',(med(i),i=13,varmax) + write(2,*)'# DSV3',(dsv(i),i=13,varmax) + + return + + end subroutine variaveis + +end module variaveis_module + +module rdf_module + + implicit none + + integer nk,nkmx + integer, allocatable :: idna(:),atp(:) + + parameter(nkmx=1000000) + + real(8) rdfcut,drdfcut,a,b,c + real(8), allocatable :: gr(:) + real(8), allocatable :: v(:,:) + real(8), allocatable :: xa(:),ya(:),za(:) + + contains + + subroutine propriedades_prepare(spctot,nat,nstp) + + implicit none + + integer i,j,k,spctot,nat,nstp + + allocate (xa(nat),ya(nat),za(nat)) + allocate (idna(nat),atp(nat)) + allocate (gr(nkmx)) + allocate (v(3,3)) + + drdfcut=0.025d0 + + do k=1,nkmx + gr(k)=0.d0 + end do + +! write(*,*)'R_cutoff','dR_cutoff' +! read(*,*)rdfcut,drdfcut + +! nk=int(rdfcut/drdfcut) + + do i=1,nstp + do k=1,5 + read(1,*) + end do + do k=1,3 + read(1,*)v(k,1),v(k,2),v(k,3) + end do + read(1,*) + do k=1,nat + read(1,*) + read(1,*) + read(1,*) + end do + if(i.eq.1)then + a=sqrt(v(1,1)**2+v(1,2)**2+v(1,3)**2) + b=sqrt(v(2,1)**2+v(2,2)**2+v(2,3)**2) + c=sqrt(v(3,1)**2+v(3,2)**2+v(3,3)**2) + else + a=min(a,sqrt(v(1,1)**2+v(1,2)**2+v(1,3)**2)) + b=min(b,sqrt(v(2,1)**2+v(2,2)**2+v(2,3)**2)) + c=min(c,sqrt(v(3,1)**2+v(3,2)**2+v(3,3)**2)) + end if + end do + + rdfcut=0.5d0*min(a,min(b,c)) + + nk=int(rdfcut/drdfcut) + + rewind(1) + + return + + end subroutine propriedades_prepare + + subroutine rdf_calc(spctot,nstp,nat) + + implicit none + + integer nstp,nat,k,i,spctot,spct(3) + real(8) lx + + call propriedades_prepare(spctot,nat,nstp) + + do i=1,nstp + do k=1,5 + read(1,*) + end do + do k=1,3 + read(1,*)v(k,1),v(k,2),v(k,3) + end do + read(1,*) + do k=1,nat + read(1,*)idna(k),atp(k),lx,lx,xa(k),ya(k),za(k) + read(1,*) + read(1,*) + end do + call rdf(nat) + end do + + do i=1,3 + spct(i)=0 + do k=1,nat + if(atp(k).eq.i)spct(i)=spct(i)+1 + end do + end do + + call rdf_final(spctot,nstp,nat,spct) + + return + + end subroutine rdf_calc + + subroutine rdf(natom) + + implicit none + + integer i,j,k,l,ll,natom + real(8) xvz,yvz,zvz,dr,rr,sum,drr + + drr=drdfcut + + rr=0.d0 + do k=1,nk + do i=1,natom + do j=1,natom + if(j.eq.i)cycle + if(atp(i).eq.1.and.atp(j).eq.1)then + call mic(i,j,xvz,yvz,zvz) + dr=sqrt(xvz**2+yvz**2+zvz**2) + if(rr.gt.(dr-0.5d0*drr))then + if(rr.le.(dr+0.5d0*drr))gr(k)=gr(k)+1.d0 + end if + end if + end do + end do + rr=rr+drr + end do + + return + + end subroutine rdf + + subroutine rdf_final(spctot,nstp,natom,spct) + + implicit none + + integer i,j,k,spctot,natom,nstp,spct(3) + real(8) rr,drr,vol + + drr=drdfcut + + rr=0.0d0 + do k=1,nk + vol=4*3.14d0*((rr+0.5d0*drr)**3-(rr-0.5d0*drr)**3)/3.d0 + gr(k)=gr(k)*a*b*c/(vol*nstp*spct(1)*spct(1)) + rr=rr+drr + end do + + rr=0.0d0 + do k=1,nk + write(2,*)rr,gr(k) + rr=rr+drr + end do + + return + + end subroutine rdf_final + + subroutine mic(i,j,xvz,yvz,zvz) + !************************************************************************** + !subrotina responsavel por aplicar a tecnica minimum image convention * + !************************************************************************** + implicit none + + integer i,j + real(8) xx,yy,zz,xvz,yvz,zvz + + xx=v(1,1)+v(2,1)+v(3,1) + yy=v(1,2)+v(2,2)+v(3,2) + zz=v(1,3)+v(2,3)+v(3,3) + + xvz=(xa(j)-xa(i))-xx*int(2.d0*(xa(j)-xa(i))/xx) + yvz=(ya(j)-ya(i))-yy*int(2.d0*(ya(j)-ya(i))/yy) + zvz=(za(j)-za(i))-zz*int(2.d0*(za(j)-za(i))/zz) + + return + + end subroutine mic + +end module rdf_module + +program tbmc + + use rdf_module + use variaveis_module + + implicit none + + integer nstp,nvar,nat,spctot,nopt + real(8) dtime + + open(1,file='TBMD.md',status='old') + open(2,file='TBMD.dat',status='unknown') + + read(1,*)nstp,dtime,nvar,nat,spctot + + write(*,*)'RDF -> 1' + write(*,*)'Medias -> 2' + + read(*,*)nopt + + select case(nopt) + case(1) + call rdf_calc(spctot,nstp,nat) + case(2) + call variaveis(nstp,nat) + end select + +end program tbmc