diff --git a/docs/source/input/SiH2_XY2_MORSE_COS_step1.inp b/docs/source/input/SiH2_XY2_MORSE_COS_step1.inp new file mode 100644 index 0000000..fafb222 --- /dev/null +++ b/docs/source/input/SiH2_XY2_MORSE_COS_step1.inp @@ -0,0 +1,390 @@ +mem 8 gb + +( CALCULATION OF VIBRATION ENERGIES FOR XY2 MOLECULE ) +( SiH2 from Per Jensen-Polyanskii paper ) +( 2006, Morbid type PES ) + +KinOrder 6 (Max order in the kinetic energy expansion) +PotOrder 8 (Max order in the potential energy expansion) + +Natoms 3 (Number of atoms) +Nmodes 3 (Number of modes = 3*Natoms-6) + +(ACTIVE SPACE CUTOFFS:) +PRIMITIVES + Npolyads 24 (how many polyads we calculate) + enercut 78000.0 (energy cut in the primitive matrix for the diagonalization) + END + +CONTRACTION + Npolyads 24 (how many polyads we calculate) + enercut 30000.0 (energy cut in the primitive matrix for the diagonalization) + degeneracy 1e-1 (threashold to define degeneracy) + sample_points 60 + sample_attempts 500 + symm_toler 1e-5 + coeff_thresh 1e-16 ( rotsym euler ) +END + +SYMGROUP C2v(M) + + +DIAGONALIZER + SYEV +end + + + +verbose 5 + + +dstep 2.0e-03 (finite difference element for each mode ) +COORDS linear (type of the internal coordinates: linear or local) +TRANSFORM r-rho-z (r-rho ( xi(chi): harmonic, linear, r-s-delta, r-s-rho, r-alpha-tau, r-rho see molecule.f90)) +MOLTYPE XY2 (Identifying type of the Molecule (e.g. XY3)) +MOLECULE SiH2 (Identifying the Molecule, e.g. PH3, BiH3 - optional) +REFER-CONF NON-RIGID (Reference configuarion: RIGID or NON-RIGID) + + +ZMAT + Si 0 0 0 0 27.97692654 + H 1 0 0 0 1.007825032 + H 1 2 0 0 1.007825032 +end + + +DIAGONALIZER + SYEV +end + + +CHECK_POINT + ascii + kinetic save + potential save + external save + basis_set save + contract save + matelem save split + extmatelem save split + eigenfunc save +END + + (type chi_kin chi_pot) +BASIS + 0,'JKtau', Jrot 0 + 1,'numerov','linear', 'morse', range 0, 12, r 8, resc 2.0, points 3000,borders -0.8,1.40 + 1,'numerov','linear', 'morse', range 0, 12, r 8, resc 2.0, points 3000,borders -0.8,1.40 + 2,'numerov','linear', 'linear', range 0, 24, r 8, resc 1.0, points 3000,borders 10.0,160.0 deg +END + + + + +EQUILIBRIUM +re 9 1.5144017558 +re 9 1.5144017558 +alphae 9 92.00507388 DEG +end + + +SPECPARAM +aa1 0 0.127050746200E+01 +aa1 0 0.127050746200E+01 +END + + + + +POTEN (SiH2_12.inp) +NPARAM 102 +POT_TYPE POTEN_XY2_MORSE_COS +COEFF list (powers or list) +RE13 1 0.15144017558000E+01 +ALPHAE 1 0.92005073880000E+02 +AA 1 0.12705074620000E+01 +B1 1 0.50000000000000E+06 +B2 1 0.50000000000000E+05 +G1 1 0.15000000000000E+02 +G2 1 0.10000000000000E+02 +V0 0 0.00000000000000E+00 +F_0_0_1 1 -0.11243403302598E+02 +F_1_0_0 1 -0.94842865087918E+01 +F_0_0_2 1 0.17366522840412E+05 +F_1_0_1 1 -0.25278354456474E+04 +F_1_1_0 1 0.20295521820240E+03 +F_2_0_0 1 0.38448640879698E+05 +F_0_0_3 1 0.27058767090918E+04 +F_1_0_2 0 -0.47718397149800E+04 +F_1_1_1 0 0.50643989272900E+04 +F_2_0_1 0 -0.71080928077800E+03 +F_2_1_0 0 0.10686442656800E+03 +F_3_0_0 0 -0.72070514638000E+04 +F_0_0_4 0 0.49417567611100E+04 +F_1_0_3 0 -0.19716938801800E+04 +F_1_1_2 0 0.38545573208100E+04 +F_2_0_2 0 -0.52979233109200E+04 +F_2_1_1 0 0.14785748436200E+04 +F_2_2_0 0 -0.25904183000400E+03 +F_3_0_1 0 0.61342662268000E+03 +F_3_1_0 0 -0.46592611312900E+03 +F_4_0_0 0 0.18393542757800E+04 +F_0_0_5 0 -0.19063209017700E+04 +F_1_0_4 0 0.23033427250700E+03 +F_1_1_3 0 0.44325395646700E+04 +F_2_0_3 0 0.21254773372200E+03 +F_2_1_2 0 0.24428800421200E+04 +F_2_2_1 0 0.35594648801800E+04 +F_3_0_2 0 -0.49227794443400E+04 +F_3_1_1 0 -0.62842214311200E+03 +F_3_2_0 0 -0.32341876680500E+04 +F_4_0_1 0 -0.13758439163300E+03 +F_4_1_0 0 -0.35633804676300E+04 +F_5_0_0 0 0.10354860940900E+03 +F_0_0_6 0 0.20068992646500E+04 +F_1_0_5 0 -0.14126866515900E+04 +F_1_1_4 0 -0.39429820715800E+04 +F_2_0_4 0 -0.78556151549000E+03 +F_2_1_3 0 0.13216135022200E+05 +F_2_2_2 0 0.00000000000000E+00 +F_3_0_3 0 0.28217359857200E+04 +F_3_1_2 0 -0.44208484827100E+04 +F_3_2_1 0 0.00000000000000E+00 +F_3_3_0 0 -0.75041615610400E+04 +F_4_0_2 0 -0.61237046683200E+04 +F_4_1_1 0 -0.62263984587600E+03 +F_4_2_0 0 -0.93340521983800E+03 +F_5_0_1 0 -0.21038541188900E+04 +F_5_1_0 0 -0.46030649924000E+04 +F_6_0_0 0 0.14910024255900E+04 +F_0_0_7 0 0.00000000000000E+00 +F_1_0_6 0 0.00000000000000E+00 +F_1_1_5 0 0.00000000000000E+00 +F_2_0_5 0 0.00000000000000E+00 +F_2_1_4 0 0.00000000000000E+00 +F_2_2_3 0 0.00000000000000E+00 +F_3_0_4 0 0.00000000000000E+00 +F_3_1_3 0 0.00000000000000E+00 +F_3_2_2 0 0.00000000000000E+00 +F_3_3_1 0 0.00000000000000E+00 +F_4_0_3 0 0.00000000000000E+00 +F_4_1_2 0 0.00000000000000E+00 +F_4_2_1 0 0.00000000000000E+00 +F_4_3_0 0 0.00000000000000E+00 +F_5_0_2 0 0.00000000000000E+00 +F_5_1_1 0 0.00000000000000E+00 +F_5_2_0 0 0.00000000000000E+00 +F_6_0_1 0 0.00000000000000E+00 +F_6_1_0 0 0.00000000000000E+00 +F_7_0_0 0 0.00000000000000E+00 +F_0_0_8 0 0.00000000000000E+00 +F_1_0_7 0 0.00000000000000E+00 +F_1_1_6 0 0.00000000000000E+00 +F_2_0_6 0 0.00000000000000E+00 +F_2_1_5 0 0.00000000000000E+00 +F_2_2_4 0 0.00000000000000E+00 +F_3_0_5 0 0.00000000000000E+00 +F_3_1_4 0 0.00000000000000E+00 +F_3_2_3 0 0.00000000000000E+00 +F_3_3_2 0 0.00000000000000E+00 +F_4_0_4 0 0.00000000000000E+00 +F_4_1_3 0 0.00000000000000E+00 +F_4_2_2 0 0.00000000000000E+00 +F_4_3_1 0 0.00000000000000E+00 +F_4_4_0 0 0.00000000000000E+00 +F_5_0_3 0 0.00000000000000E+00 +F_5_1_2 0 0.00000000000000E+00 +F_5_2_1 0 0.00000000000000E+00 +F_5_3_0 0 0.00000000000000E+00 +F_6_0_2 0 0.00000000000000E+00 +F_6_1_1 0 0.00000000000000E+00 +F_6_2_0 0 0.00000000000000E+00 +F_7_0_1 0 0.00000000000000E+00 +F_7_1_0 0 0.00000000000000E+00 +F_8_0_0 0 0.00000000000000E+00 +end + +DIPOLE +rank 3 +NPARAM 72 99 0 +TYPE xy2_pq_coeff +COEFF list (powers or list) +COORDS linear linear linear +Orders 6 6 6 +dstep 0.005 0.005 0.005 +Parameters +re 0 0.152000000000E+01 +alphae 0 0.945000000000E+02 +f_1_0_0 7 -0.170274198034E+01 +f_1_0_1 7 -0.122791150585E+00 +f_2_0_0 6 -0.519187500441E+00 +f_1_0_2 6 0.185415937182E+00 +f_2_0_1 6 0.715740118118E+00 +f_2_1_0 6 -0.147662628115E+00 +f_3_0_0 6 0.598556914831E+00 +f_1_0_3 5 -0.254782876878E+00 +f_2_0_2 5 -0.134608539883E+00 +f_2_1_1 5 -0.432191350340E+00 +f_3_0_1 5 0.167534918746E+00 +f_3_1_0 5 0.199877673796E+00 +f_4_0_0 5 0.241937009449E+00 +f_1_0_4 4 0.424402396399E+00 +f_2_0_3 3 0.242515351956E+00 +f_2_1_2 0 0.000000000000E+00 +f_3_0_2 3 0.165887666267E+00 +f_3_1_1 3 -0.336680525693E+00 +f_3_2_0 0 0.000000000000E+00 +f_4_0_1 1 -0.547718047522E+00 +f_4_1_0 0 0.000000000000E+00 +f_5_0_0 0 0.000000000000E+00 +f_1_0_5 0 0.000000000000E+00 +f_2_0_4 0 0.000000000000E+00 +f_2_1_3 0 0.000000000000E+00 +f_3_0_3 0 0.000000000000E+00 +f_3_1_2 0 0.000000000000E+00 +f_3_2_1 0 0.000000000000E+00 +f_4_0_2 0 0.000000000000E+00 +f_4_1_1 0 0.000000000000E+00 +f_4_2_0 0 0.000000000000E+00 +f_5_0_1 0 0.000000000000E+00 +f_5_1_0 0 0.000000000000E+00 +f_6_0_0 0 0.000000000000E+00 +f_1_0_6 0 0.000000000000E+00 +f_2_0_5 0 0.000000000000E+00 +f_2_1_4 0 0.000000000000E+00 +f_3_0_4 0 0.000000000000E+00 +f_3_1_3 0 0.000000000000E+00 +f_3_2_2 0 0.000000000000E+00 +f_4_0_3 0 0.000000000000E+00 +f_4_1_2 0 0.000000000000E+00 +f_4_2_1 0 0.000000000000E+00 +f_4_3_0 0 0.000000000000E+00 +f_5_0_2 0 0.000000000000E+00 +f_5_1_1 0 0.000000000000E+00 +f_5_2_0 0 0.000000000000E+00 +f_6_0_1 0 0.000000000000E+00 +f_6_1_0 0 0.000000000000E+00 +f_7_0_0 0 0.000000000000E+00 +f_1_0_7 0 0.000000000000E+00 +f_2_0_6 0 0.000000000000E+00 +f_2_1_5 0 0.000000000000E+00 +f_3_0_5 0 0.000000000000E+00 +f_3_1_4 0 0.000000000000E+00 +f_3_2_3 0 0.000000000000E+00 +f_4_0_4 0 0.000000000000E+00 +f_4_1_3 0 0.000000000000E+00 +f_4_2_2 0 0.000000000000E+00 +f_4_3_1 0 0.000000000000E+00 +f_5_0_3 0 0.000000000000E+00 +f_5_1_2 0 0.000000000000E+00 +f_5_2_1 0 0.000000000000E+00 +f_5_3_0 0 0.000000000000E+00 +f_6_0_2 0 0.000000000000E+00 +f_6_1_1 0 0.000000000000E+00 +f_6_2_0 0 0.000000000000E+00 +f_7_0_1 0 0.000000000000E+00 +f_7_1_0 0 0.000000000000E+00 +f_8_0_0 0 0.000000000000E+00 +f_4_1_3 0 0.000000000000E+00 +re 0 0.152000000000E+01 +alphae 0 0.945000000000E+03 +a 0 0.000000000000E+00 +dummy 0 0.000000000000E+00 +xp(1) 9 0.176547582678E+01 +x0x0x1 8 -0.492245503195E+01 +x1x0x0 7 -0.193070832496E+01 +x0x0x2 7 0.900424248416E+01 +x0x2x0 7 0.114484321174E+01 +x1x0x1 7 -0.116840841811E+01 +x2x0x0 7 -0.101953882061E+01 +x0x0x3 6 -0.152151621639E+02 +x0x2x1 6 -0.837666739155E+00 +x1x0x2 6 0.397478800603E+01 +x1x2x0 5 0.281068202441E+01 +x2x0x1 6 0.243991950651E+00 +x3x0x0 5 0.196974447274E+00 +x0x0x4 5 0.166479435952E+02 +x0x2x2 0 0.000000000000E+00 +x0x4x0 5 -0.497159842991E+01 +x1x0x3 4 -0.534938935806E+01 +x1x2x1 4 0.923022674829E+00 +x2x0x2 0 0.000000000000E+00 +x2x2x0 4 0.100550735735E+01 +x3x0x1 4 0.384995296047E+00 +x4x0x0 4 0.558426042004E+00 +x0x0x5 1 -0.100853543301E+02 +x0x2x3 4 0.269748146577E+00 +x0x4x1 3 0.249589764086E+01 +x1x0x4 1 0.516062001854E+01 +x1x2x2 3 -0.259020975470E+01 +x1x4x0 0 0.000000000000E+00 +x2x0x3 3 -0.146192512676E+01 +x2x2x1 0 0.000000000000E+00 +x3x0x2 2 0.385983072014E+00 +x3x2x0 2 -0.105976335828E+01 +x4x0x1 2 -0.769565825722E+00 +x5x0x0 2 0.205422125242E+00 +x0x0x6 1 0.256894089673E+01 +x0x2x4 1 -0.185570046407E+00 +x0x4x2 0 0.000000000000E+00 +x0x6x0 1 -0.198458761496E+01 +x1x0x5 1 0.150218813897E+01 +x1x2x3 0 0.000000000000E+00 +x1x4x1 1 0.758176192395E+00 +x2x0x4 1 -0.639532381955E+00 +x2x2x2 0 0.000000000000E+00 +x2x4x0 1 -0.273311819911E+01 +x3x0x3 1 0.767466013533E+00 +x3x2x1 1 0.104806493873E+01 +x4x0x2 0 0.000000000000E+00 +x4x2x0 0 0.000000000000E+00 +x5x0x1 0 0.000000000000E+00 +x6x0x0 1 -0.209765236321E+00 +x0x0x7 0 0.000000000000E+00 +x0x2x5 0 0.000000000000E+00 +x0x4x3 0 0.000000000000E+00 +x0x6x1 0 0.000000000000E+00 +x1x0x6 0 0.000000000000E+00 +x1x2x4 0 0.000000000000E+00 +x1x4x2 0 0.000000000000E+00 +x1x6x0 0 0.000000000000E+00 +x2x0x5 0 0.000000000000E+00 +x2x2x3 0 0.000000000000E+00 +x2x4x1 0 0.000000000000E+00 +x3x0x4 0 0.000000000000E+00 +x3x2x2 0 0.000000000000E+00 +x3x4x0 0 0.000000000000E+00 +x4x0x3 0 0.000000000000E+00 +x4x2x1 0 0.000000000000E+00 +x5x0x2 0 0.000000000000E+00 +x5x2x0 0 0.000000000000E+00 +x6x0x1 0 0.000000000000E+00 +x7x0x0 0 0.000000000000E+00 +x0x0x8 0 0.000000000000E+00 +x0x2x6 0 0.000000000000E+00 +x0x4x4 0 0.000000000000E+00 +x0x6x2 0 0.000000000000E+00 +x0x8x0 0 0.000000000000E+00 +x1x0x7 0 0.000000000000E+00 +x1x2x5 0 0.000000000000E+00 +x1x4x3 0 0.000000000000E+00 +x1x6x1 0 0.000000000000E+00 +x2x0x6 0 0.000000000000E+00 +x2x2x4 0 0.000000000000E+00 +x2x4x2 0 0.000000000000E+00 +x2x6x0 0 0.000000000000E+00 +x3x0x5 0 0.000000000000E+00 +x3x2x3 0 0.000000000000E+00 +x3x4x1 0 0.000000000000E+00 +x4x0x4 0 0.000000000000E+00 +x4x2x2 0 0.000000000000E+00 +x4x4x0 0 0.000000000000E+00 +x5x0x3 0 0.000000000000E+00 +x5x2x1 0 0.000000000000E+00 +x6x0x2 0 0.000000000000E+00 +x6x2x0 0 0.000000000000E+00 +x7x0x1 0 0.000000000000E+00 +x8x0x0 0 0.000000000000E+00 +end + + diff --git a/docs/source/potentials.rst b/docs/source/potentials.rst index 7699897..7b35a20 100644 --- a/docs/source/potentials.rst +++ b/docs/source/potentials.rst @@ -24,21 +24,30 @@ The ``Potential`` (``Poten``) block used to specify a PEF, has the following gen :: - POTENTIAL - NPARAM 99 - POT_TYPE poten_xy2_tyuterev - COEFF list - b1 0 0.80000000000000E+06 - b2 0 0.80000000000000E+05 - g1 0 0.13000000000000E+02 - g2 0 0.55000000000000E+01 - f000 0 0.00000000000000E+00 - f001 1 0.25298724728304E+01 - f100 1 0.76001446034650E+01 + POTEN + NPARAM 102 + POT_TYPE POTEN_XY2_MORSE_COS + COEFF list (powers or list) + RE13 1 0.15144017558000E+01 + ALPHAE 1 0.92005073880000E+02 + AA 1 0.12705074620000E+01 + B1 1 0.50000000000000E+06 + B2 1 0.50000000000000E+05 + G1 1 0.15000000000000E+02 + G2 1 0.10000000000000E+02 + V0 0 0.00000000000000E+00 + F_0_0_1 1 -0.11243403302598E+02 + F_1_0_0 1 -0.94842865087918E+01 + F_0_0_2 1 0.17366522840412E+05 + F_1_0_1 1 -0.25278354456474E+04 + F_1_1_0 1 0.20295521820240E+03 + F_2_0_0 1 0.38448640879698E+05 + F_0_0_3 1 0.27058767090918E+04 + F_1_0_2 0 -0.47718397149800E+04 ... end -For an example, see `h2s_step1.inp `_ where this PES is used. +For an example, see `SiH2_XY2_MORSE_COS_step1.inp `_ where this PES is used. Here ``NPARAM`` is used to specify the number of parameters used to define the PES. ``POT_TYPE`` is the name of the potential energy surface being used which is defined in the ``pot_*.f90 file``. The keywords ``COEFF`` indicates if the potential contains a list of parameter values (``LIST``) or values with the corresponding expansion powers (``POWERS``), e.g. (for H\ :sub:`2`\ CO): :: @@ -196,11 +205,40 @@ For an example, see `SO2_morbid_step1.inp `_. This PES was used in [21ClYu}_ . + + + ``POTEN_XY2_TYUTEREV`` ^^^^^^^^^^^^^^^^^^^^^^ -For description and example see above. -The input file example is `h2s_step1.inp `_ where this PES is used. +``POTEN_XY2_TYUTEREV`` is the essentially the same PES as ``POTEN_XY2_MORSE_COS``, with the difference that the ``POTEN`` input part does not contain the structural parameters: + + +:: + + POTENTIAL + NPARAM 99 + POT_TYPE poten_xy2_tyuterev + COEFF list + b1 0 0.80000000000000E+06 + b2 0 0.80000000000000E+05 + g1 0 0.13000000000000E+02 + g2 0 0.55000000000000E+01 + f000 0 0.00000000000000E+00 + f001 1 0.25298724728304E+01 + f100 1 0.76001446034650E+01 + ... + end + + +Using the structural parameters in the ``POTEN`` section is important for PES refinements, see the corresponding section for details. +The input file example is `h2s_step1.inp `_ . + + ``poten_co2_ames1`` @@ -281,7 +319,7 @@ The vibrational coordinates are \xi_3 &= \alpha-\alpha_{\rm eq}, \end{split} -where the internal stretching coordinates :math:`r_1 = r_1^{\rm eq} `, :math:`r_2 = r_2^{\rm eq} `, the interbond angle :math:`\alpha = \angle({\rm e})`, and the equilibrium parameters are :math:`r_1^{\rm eq}`, :math:`r_2^{\rm eq}` and :math:`\alpha_{\rm eq}`. Note that the exponent :math:`k` associated with the bending coordinate :math:`\xi_3` assumes only even values because of the symmetry of the XYZ molecule. +where the internal stretching coordinates :math:`r_1 = r_1^{\rm eq}`\ , :math:`r_2 = r_2^{\rm eq}`\ , the interbond angle :math:`\alpha = \angle({\rm e})`\ , and the equilibrium parameters are :math:`r_1^{\rm eq}`, :math:`r_2^{\rm eq}` and :math:`\alpha_{\rm eq}`. Note that the exponent :math:`k` associated with the bending coordinate :math:`\xi_3` assumes only even values because of the symmetry of the XYZ molecule. The input file example is `CaOH_Koput_step1.inp `_ where this PES is used. diff --git a/docs/source/references.rst b/docs/source/references.rst index 0929139..435f49c 100644 --- a/docs/source/references.rst +++ b/docs/source/references.rst @@ -67,3 +67,4 @@ References .. [17HuScFr] X. Huang, D.W. Schwenke, R.S. Freedman, ΠΆ.J. Lee, J. Quant. Spectrosc. Radiat. Transf., 203, 224 (2017), Ames-2016 line lists for 13 isotopologues of CO\ :sub:`2`\ : Updates, consistency, and remaining issues. +.. [21ClYu] V.H. J. Clark and S.N. Yurchenko. Phys. Chem. Chem. Phys., 23, 11990 (2021), Modelling the non-local thermodynamic equilibrium spectra of silylene (SiH\ :sub:`2`\ ).