Merge remote-tracking branch 'origin/master'

Former-commit-id: 14101e0482ee031730ab4d327ec249b6b7507126 [formerly 7b7937a] Former-commit-id: e6d66751b68302076d93d2f760a95f6c871c2b63
materialsproject · Dec 16, 2013 · 93b60bf · 93b60bf
2 parents 38295bf + 88d1368
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diff --git a/circle.yml b/circle.yml
@@ -9,6 +9,8 @@ dependencies:
 test:
   override:
     - mv pymatgen pmg
-    - nosetests:
+    - nosetests -v:
         environment:
-            PATH: $PATH:`pwd`/cmd_line/enum/Linux_64bit:`pwd`/cmd_line/bader/Linux_64bit
+            PATH: $PATH:`pwd`/cmd_line/enum/Linux_64bit:`pwd`/cmd_line/bader/Linux_64bit:`pwd`/cmd_line/gulp/Linux_64bit:`pwd`/cmd_line/aconvasp/Linux_64bit
+            GULP_LIB: /`pwd`/cmd_line/gulp/Libraries
+            PYTHONPATH: $PYTHONPATH:/usr/lib/python2.7/dist-packages/
diff --git a/cmd_line/aconvasp/Darwin_64bit/aconvasp.REMOVED.git-id b/cmd_line/aconvasp/Darwin_64bit/aconvasp.REMOVED.git-id
@@ -0,0 +1 @@
+500e3b215b1277c64e2362406920b949a03d2a29
diff --git a/cmd_line/aconvasp/Linux_64bit/aconvasp.REMOVED.git-id b/cmd_line/aconvasp/Linux_64bit/aconvasp.REMOVED.git-id
@@ -0,0 +1 @@
+692821b6c9afccfd27a298c26ded50ec50347a92
diff --git a/cmd_line/gulp/Libraries/belashchenko.lib b/cmd_line/gulp/Libraries/belashchenko.lib
@@ -0,0 +1,74 @@
+#
+#  Belashchenko EAM potential for Na
+#
+#  High. Temp., 47, 494-507 (2009)
+#
+species
+Na core 0.0
+#
+#  EAM potential
+#
+many 
+Na core Na core 10.78
+eam_fun belashchenko
+Na core 0.90 0.80 0.70 
+        0.62 0.28 1.17 2.60
+       -0.3314 1.15 1.42
+        0.1619 -0.170 -0.275 0.600
+        0.8800  5.000 -0.100 0.335
+eam_den expo 0
+Na core Na core 3.4418 1.0245 0.0 
+#
+#  Two-body potential
+#
+buckingham
+Na core Na core 16.7666377 0.833333333 0.0 0.0 2.5499999999
+polynomial 
+5
+Na core Na core 0.35805506 -2.8231320 12.574037 324.38852 &
+                1675.1389 2599.4679 2.80 &
+                2.55 2.7999999999
+polynomial 
+3
+Na core Na core 0.12708218 -0.78856218 1.4613397 -23.646932 2.95 &
+                2.80 2.9499999999
+polynomial 
+6
+Na core Na core -0.11093583 -0.30139562 -0.57444694 -7.6710592 &
+                -29.513198 -53.353203 -35.242442 3.45 &
+                2.95 3.4499999999
+polynomial 
+6
+Na core Na core -0.18380286 -0.031204076 0.66662912 4.8636249 &
+                20.310489 37.538781 25.743498 3.95 &
+                3.45 3.9499999999
+polynomial 
+6
+Na core Na core -0.17446597 0.094991311 0.61158912 3.8291921 &
+                12.551371 18.518679 10.122143 4.45 &
+                3.95 4.4499999999
+polynomial 
+6
+Na core Na core -0.13020295 0.087927282 -0.56735449 -5.2796190 &
+                -19.751878 -33.862967 -21.896864 4.95 &
+                4.45 4.9499999999
+polynomial 
+6
+Na core Na core -0.073686510 0.13220064 0.75321670 6.8207026 &
+                26.093839 45.498140 29.748444 5.45 &
+                4.95 5.4499999999
+polynomial 
+6
+Na core Na core -0.026368676 0.079378478 -0.076503428 -0.64246319 &
+                -3.6612803 -8.7641368 -7.2870333 5.95 &
+                5.45 5.9499999999
+polynomial 
+6
+Na core Na core 0.028540069 -0.0019879458 0.0056904208 0.080223638 &
+                0.099188093 0.061698530 0.014612381 7.45 &
+                5.95 7.4499999999
+polynomial 
+6
+Na core Na core 0.73629497d-4 0.0 -0.40257317d-2 -0.5299351d-2 &
+                -0.167443d-2 -0.4226847d-3 -0.65802071d-4 10.78 &
+                7.45 10.7799999999
diff --git a/cmd_line/gulp/Libraries/bks.lib b/cmd_line/gulp/Libraries/bks.lib
@@ -0,0 +1,24 @@
+#
+#  BKS library - rigid ion potentials for silica
+#
+#  Reference:
+#  B.W.H. van Beest et al, Phys. Rev. Lett., 64, 1955 (1990)
+#
+#  NOTE: Because of the large C6 terms (which are unphysical
+#        and the short cutoff given in the paper, there will
+#        be lots of problems associated with potential 
+#        discontinuities if using this library. It should also
+#        be noted that the SiO2 potential is known to give the
+#        incorrect ground state polymorph for silica. You have
+#        been warned!
+#
+species
+Al    core  1.4
+Si    core  2.4
+P     core  3.4
+O     core -1.2
+buck
+Al core O core 16008.5345 0.208478  130.5669 0.0 10.0
+Si core O core 18803.7572 0.205205  133.5381 0.0 10.0
+P  core O core  9034.2080 0.192642   19.8793 0.0 10.0
+O  core O core  1338.7730 0.362319  175.0000 0.0 10.0
diff --git a/cmd_line/gulp/Libraries/bresme_water.lib b/cmd_line/gulp/Libraries/bresme_water.lib
@@ -0,0 +1,27 @@
+#
+#  Central Force Model for water by Fernando Bresme. 
+#
+#  F. Bresme, J. Chem. Phys., 115, 7564 (2001)
+#
+species
+O  core -0.65966
+H  core  0.32983
+#
+#  Intramolecular potentials
+#
+#  O-H target : K = 49.7635564 eV/Ang**2 and r0 = 0.9584
+#  H-H target : K = 11.1548260 eV/Ang**2 and r0 = 1.5151
+#
+cfm_harm
+O core H core 56.88150901 1.018365407784 1.45 0.02 0.0 6.0
+H core H core 10.25399858 1.448548221520 1.88 0.02 0.0 6.0
+#
+#  Intermolecular potentials
+#
+cfm_power kcal
+O core O core 23700.0 8.8591 1.0 -0.02 0.0 14.0
+cfm_gauss kcal
+O core O core -0.25 4.0 3.4 12.0 0.02 0.0 14.0
+O core O core -0.20 1.5 4.5 12.0 0.02 0.0 14.0
+cfm_fermi kcal
+O core H core -4.0 5.49305 2.2 1.45 0.02 0.0 6.0
diff --git a/cmd_line/gulp/Libraries/bush.lib b/cmd_line/gulp/Libraries/bush.lib
@@ -0,0 +1,79 @@
+#
+#  BUSH -library of potentials for GULP
+#
+#  from T.S.Bush, J.D.Gale, C.R.A.Catlow and P.D. Battle
+#  J. Mater Chem., 4, 831-837 (1994)
+#
+species
+Li core  1.000
+Na core  1.000
+K  core  1.000
+Mg core  1.580
+Mg shel  0.420
+Ca core  0.719
+Ca shel  1.281
+Sr core  0.169
+Sr shel  1.831
+Ba core  0.169
+Ba shel  1.831
+Fe core  1.971
+Fe shel  1.029
+Ti core  2.332
+Ti shel  1.668
+Al core  0.043
+Al shel  2.957
+Ga core  3.000
+Y  core  3.000
+La core  5.149
+La shel -2.149
+Pr core  1.678
+Pr shel  1.322
+Nd core  1.678
+Nd shel  1.322
+Gd core -0.973
+Gd shel  3.973
+Eu core -0.991
+Eu shel  3.991
+Tb core -0.972
+Tb shel  3.972
+Yb core -0.278
+Yb shel  3.278
+O  core  0.513
+O  shel -2.513
+buckingham
+Li core O shel   426.480 0.3000  0.00 0.0 10.0
+Na core O shel  1271.504 0.3000  0.00 0.0 10.0
+K  core O shel  3587.570 0.3000  0.00 0.0 10.0
+Mg shel O shel  2457.243 0.2610  0.00 0.0 10.0
+Ca shel O shel  2272.741 0.2986  0.00 0.0 10.0
+Sr shel O shel  1956.702 0.3252  0.00 0.0 10.0
+Ba shel O shel  4818.416 0.3067  0.00 0.0 10.0
+Fe shel O shel  3219.335 0.2641  0.00 0.0 10.0
+Ti shel O shel  2088.107 0.2888  0.00 0.0 10.0
+Al shel O shel  2409.505 0.2649  0.00 0.0 10.0
+Ga core O shel  2339.776 0.2742  0.00 0.0 10.0
+Y  core O shel  1519.279 0.3291  0.00 0.0 10.0
+La shel O shel  5436.827 0.2939  0.00 0.0 10.0
+Pr shel O shel 13431.118 0.2557  0.00 0.0 10.0
+Nd shel O shel 13084.217 0.2550  0.00 0.0 10.0
+Gd shel O shel   866.339 0.3770  0.00 0.0 10.0
+Eu shel O shel   847.868 0.3791  0.00 0.0 10.0
+Tb shel O shel   845.137 0.3750  0.00 0.0 10.0
+Yb shel O shel   991.029 0.3515  0.00 0.0 10.0
+O  shel O shel    25.410 0.6937 32.32 0.0 12.0
+spring
+Mg 349.95
+Ca  34.05
+Sr  21.53
+Ba  34.05
+Fe 179.58
+Ti 253.60
+Al 403.98
+La 173.90
+Pr 302.36
+Nd 302.35
+Gd 299.96
+Eu 304.92
+Tb 299.98
+Yb 308.91
+O   20.53
diff --git a/cmd_line/gulp/Libraries/carbonate.lib b/cmd_line/gulp/Libraries/carbonate.lib
@@ -0,0 +1,98 @@
+#
+#   POTENTIALS FOR CALCITE : 
+#
+#   Rohl, Wright and Gale, Am. Miner., 88, 921-925 (2003)
+#   Austen, Wright, Slater and Gale, PCCP, 7, 4150 - 4156 (2005)
+#
+#   NOTE : requires a version of GULP later than 1.3 
+#
+#
+#  This option specifies that Coulomb interactions within molecules are excluded
+#
+keyword mole
+#
+#  The following is a list of the charges for each species
+#
+species
+Ca    core  2.00000000 
+Mg    core  2.00000000 
+Fe    core  2.00000000 
+Cd    core  2.00000000 
+Mn    core  2.00000000 
+Ni    core  2.00000000 
+Zn    core  2.00000000 
+Co    core  2.00000000 
+C     core  1.34353898 
+O     core  1.01848700 
+O     shel -2.13300000 
+#
+#  The following are the parameters of the Buckingham potential where the numbers
+#  are:
+#  A rho C rmin rmax with units eV, Angstroms**-1, eV**Angs**6, Angs, Angs, respectively
+#
+#  E = A.exp(-r/rho) - C/r**6 for rmin < r < rmax
+#
+#  intra => only acts within a molecule
+#  inter => only acts between molecules
+#
+buck intra     
+O     core O     core  4030.3000     0.245497 0.00000000      0.00  2.50 
+buck     
+Ca    core O     shel  2154.0600     0.289118 0.00000000      0.00 10.00
+Mg    core O     shel  1039.5900     0.289329 0.00000000      0.00 10.00
+Fe    core O     shel  1550.1075     0.265070 0.00000000      0.00 10.00
+Cd    core O     shel  3117.3763     0.256300 0.00000000      0.00 10.00
+Mn    core O     shel  1440.6645     0.272680 0.00000000      0.00 10.00
+Ni    core O     shel  1176.7798     0.266610 0.00000000      0.00 10.00
+Zn    core O     shel   741.1401     0.289100 0.00000000      0.00 10.00
+Co    core O     shel   788.8089     0.286300 0.00000000      0.00 10.00
+Ca    core C     core 120000000.000  0.120000 0.00000000      0.00 10.00 
+Mg    core C     core  26164795.400  0.120000 0.00000000      0.00 10.00 
+Fe    core C     core  90909090.910  0.120000 0.00000000      0.00 10.00 
+Cd    core C     core 117575757.600  0.120000 0.00000000      0.00 10.00 
+Mn    core C     core  98181818.180  0.120000 0.00000000      0.00 10.00 
+Ni    core C     core 100606060.600  0.120000 0.00000000      0.00 10.00 
+Zn    core C     core  89696969.700  0.120000 0.00000000      0.00 10.00 
+Co    core C     core  95757575.760  0.120000 0.00000000      0.00 10.00 
+buck inter     
+O     shel O     shel  64242.454     0.198913  21.843570      0.00 15.00
+#
+#  The following are the parameters of the Morse potential
+#
+#  D0 a r0 Coulomb_flag with units eV, Angs**-1, Angstroms and none, respectively
+#
+morse intra bond
+C     core O     core 5.0000000     2.5228      1.19820  0.0000 
+#
+#  The following specifies the spring constant for the shell model in eV/Angs**2
+#
+spring
+O      52.740087 
+#
+#  The following specifies the force constant and equilibrium angle for the three-body
+#  harmonic potential, in eV/rad**2 and degrees, respectively.
+#
+three bond intra
+C     core O     core O     core 1.7995     120.00  
+#
+#  The following specifies the out of plane potential of form :
+#
+#  E = 1/2 K2*r**2 + 1/12 K4*r**4
+#
+#  The values given are K2 and K4 in units of eV/Angs**2 and eV/Angs**4
+#
+outofplane bond intra
+C     cor O     cor O     cor O     cor 8.6892 360.0 
+#
+#  The covalent radius of Ca must be zero so that the molecules are correctly defined
+#
+element
+cova Ca 0.0
+cova Mg 0.0
+cova Ni 0.0
+cova Zn 0.0
+cova Co 0.0
+cova Fe 0.0
+cova Cd 0.0
+cova Mn 0.0
+end
diff --git a/cmd_line/gulp/Libraries/catlow.lib b/cmd_line/gulp/Libraries/catlow.lib
@@ -0,0 +1,49 @@
+#
+#  CATLOW library - collection of potentials based
+#  around the Catlow oxygen-oxygen potential
+#
+#  O_O2- general O2- species
+#  O_OH  oxygen in hydroxyl group
+#  H_OH  hydrogn in hydroxyl group
+#
+#  References:
+#  (1) K.P.Schroder, J.Sauer, M.Leslie, C.R.A.Catlow and
+#      J.M.Thomas, Chem. Phys. Lett., 188 (1992) 320.
+#  (2) J.D.Gale and N.J.Henson, JCS Faraday Trans., 90
+#      (1994) 3175.
+#  (3) J.D.Gale, unpublished results - non-zeolite potentials
+#      are relax fitted to structure and any available properties
+#      for the relevant binary oxide
+#
+species
+Na    core  1.00000
+Mg    core  2.00000
+Al    core  3.00000
+Si    core  4.00000
+P     core  5.00000
+O_O2- core  0.86902
+O_O2- shel -2.86902
+O_OH  core -1.42600
+H_OH  core  0.42600
+buckingham
+buck
+Na core    O_O2- shel   468.002 0.35771  0.00000 0.0 10.0
+Mg core    O_O2- shel   946.627 0.31813  0.00000 0.0 10.0
+Al core    O_O2- shel  1460.300 0.29912  0.00000 0.0 10.0
+Al core    O_OH  core  1142.678 0.29912  0.00000 0.0 10.0
+Si core    O_O2- shel  1283.907 0.32052 10.66158 0.0 10.0
+Si core    O_OH  core   983.557 0.32052 10.66158 0.0 10.0
+P  core    O_O2- shel   877.340 0.35940  0.00000 0.0 10.0
+O_O2- shel O_O2- shel 22764.000 0.14900 27.87900 0.0 12.0
+O_O2- shel O_OH  core 22764.000 0.14900 27.87900 0.0 12.0
+O_OH  core O_OH  core 22764.000 0.14900 27.87900 0.0 12.0
+O_O2- shel H_OH  core   311.970 0.25000  0.00000 0.0 12.0
+morse
+O_OH  core H_OH  core 7.0525 2.1986 0.9485 1.0 1.4
+spring
+O_O2-  74.92
+three
+Si core O_O2- shel O_O2- shel 2.09724 109.47 1.9 1.9 3.5
+Si core O_OH  core O_O2- shel 2.09724 109.47 1.9 1.9 3.5
+Al core O_O2- shel O_O2- shel 2.09724 109.47 1.9 1.9 3.5
+Al core O_OH  core O_O2- shel 2.09724 109.47 1.9 1.9 3.5