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Add test inputs for common 3-site water models

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This commit is contained in:
Matthias Krack 2024-01-15 18:51:03 +01:00
parent 3b6314e491
commit dcfa1d54c0
10 changed files with 900 additions and 0 deletions
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47
data/forcefield_section/H2O/SPC.sec Normal file
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# SPC water
# H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem. 91, 6269 (1987)
# https://doi.org/10.1021/j100308a038
# Note: This force field requires a correpsonding &G3X3 constraint section
# in &MOTION / &CONSTRAINT
&FORCEFIELD
&BEND
ATOMS HW OW HW
K [kcalmol*rad^-2] 0.0
KIND harmonic
THETA0 [deg] 109.47
&END BEND
&BOND
ATOMS OW HW
K [kcalmol*Angstrom^-2] 0.0
KIND harmonic
R0 [Angstrom] 1.000
&END BOND
&CHARGE
ATOM OW
CHARGE -0.820
&END CHARGE
&CHARGE
ATOM HW
CHARGE +0.410
&END CHARGE
&NONBONDED
&LENNARD-JONES
ATOMS HW HW
EPSILON [kcalmol] 0.0
SIGMA [Angstrom] 1.0
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS OW HW
EPSILON [kcalmol] 0.0
SIGMA [Angstrom] 1.0
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS OW OW
EPSILON [kJmol] 0.65016958
SIGMA [Angstrom] 3.16555789
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&END NONBONDED
&END FORCEFIELD

47
data/forcefield_section/H2O/SPCE.sec Normal file
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# SPC/E water
# H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem. 91, 6269 (1987)
# https://doi.org/10.1021/j100308a038
# Note: This force field requires a correpsonding &G3X3 constraint section
# in &MOTION / &CONSTRAINT
&FORCEFIELD
&BEND
ATOMS HW OW HW
K [kcalmol*rad^-2] 0.0
KIND harmonic
THETA0 [deg] 109.47
&END BEND
&BOND
ATOMS OW HW
K [kcalmol*Angstrom^-2] 0.0
KIND harmonic
R0 [Angstrom] 1.000
&END BOND
&CHARGE
ATOM OW
CHARGE -0.8476
&END CHARGE
&CHARGE
ATOM HW
CHARGE +0.4238
&END CHARGE
&NONBONDED
&LENNARD-JONES
ATOMS HW HW
EPSILON [kcalmol] 0.0
SIGMA [Angstrom] 1.0
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS OW HW
EPSILON [kcalmol] 0.0
SIGMA [Angstrom] 1.0
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS OW OW
EPSILON [kJmol] 0.65016958
SIGMA [Angstrom] 3.16555789
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&END NONBONDED
&END FORCEFIELD

47
data/forcefield_section/H2O/TIP3P.sec Normal file
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# TIP3P water
# M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)
# https://doi.org/10.1063/1.481505
# Note: This force field requires a correpsonding &G3X3 constraint section
# in &MOTION / &CONSTRAINT
&FORCEFIELD
&BEND
ATOMS HW OW HW
K [kcalmol*rad^-2] 0.0
KIND harmonic
THETA0 [deg] 104.52
&END BEND
&BOND
ATOMS OW HW
K [kcalmol*Angstrom^-2] 0.0
KIND harmonic
R0 [Angstrom] 0.9572
&END BOND
&CHARGE
ATOM OW
CHARGE -0.834
&END CHARGE
&CHARGE
ATOM HW
CHARGE +0.417
&END CHARGE
&NONBONDED
&LENNARD-JONES
ATOMS HW HW
EPSILON [kcalmol] 0.0
SIGMA [Angstrom] 1.0
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS OW HW
EPSILON [kcalmol] 0.0
SIGMA [Angstrom] 1.0
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS OW OW
EPSILON [kcalmol] 0.1521
SIGMA [Angstrom] 3.15061
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&END NONBONDED
&END FORCEFIELD

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data/forcefield_section/H2O/TIP3P_FLEXIBLE.sec Normal file
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# TIP3P flexible water
# M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)
# https://doi.org/10.1063/1.481505
&FORCEFIELD
&BEND
ATOMS HW OW HW
K [kcalmol*rad^-2] 110.0
KIND harmonic
THETA0 [deg] 104.52
&END BEND
&BOND
ATOMS OW HW
K [kcalmol*Angstrom^-2] 900.0
KIND harmonic
R0 [Angstrom] 0.9572
&END BOND
&CHARGE
ATOM OW
CHARGE -0.834
&END CHARGE
&CHARGE
ATOM HW
CHARGE +0.417
&END CHARGE
&NONBONDED
&LENNARD-JONES
ATOMS HW HW
EPSILON [kcalmol] 0.0
SIGMA [Angstrom] 1.0
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS OW HW
EPSILON [kcalmol] 0.0
SIGMA [Angstrom] 1.0
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&LENNARD-JONES
ATOMS OW OW
EPSILON [kcalmol] 0.1521
SIGMA [Angstrom] 3.15061
RCUT [Angstrom] 12.0
&END LENNARD-JONES
&END NONBONDED
&END FORCEFIELD

179
tests/Fist/regtest-water/H2O-SPC-6x6x6.inp Normal file
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# Cubic cell with 6*6*6 = 216 H2O molecules
@SET model SPC
@SET doh 1.000000000
@SET dhh 1.632980862
@SET a 3.16
@SET na 6
@SET nb 6
@SET nc 6
@SET nh2o ${na}x${nb}x${nc}
@SET pf 10
&GLOBAL
PRINT_LEVEL medium
PROJECT H2O-${model}-${nh2o}
RUN_TYPE MD
&END GLOBAL
&MOTION
&CONSTRAINT
&G3X3
ATOMS 1 2 3
DISTANCES [Angstrom] ${doh} ${doh} ${dhh}
MOLNAME H2O
&END G3X3
&END CONSTRAINT
&MD
ENSEMBLE NpT_i
STEPS 50
TEMPERATURE [K] 300.0
TEMP_KIND on
TIMESTEP [fs] 0.5
&BAROSTAT
PRESSURE [bar] 1.0
TIMECON [fs] 1000.0
&PRINT
&ENERGY
&EACH
MD ${pf}
&END EACH
&END ENERGY
&END PRINT
&END BAROSTAT
&PRINT
&CENTER_OF_MASS on
&EACH
MD ${pf}
&END EACH
&END CENTER_OF_MASS
&ENERGY on
&EACH
MD ${pf}
&END EACH
&END ENERGY
&PROGRAM_RUN_INFO on
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&TEMP_KIND on
&EACH
MD ${pf}
&END EACH
&END TEMP_KIND
&END PRINT
&THERMOSTAT
REGION global
TYPE CSVR
&CSVR
TIMECON [fs] 100.0
&END CSVR
&END THERMOSTAT
&END MD
&PRINT
&CELL on
&EACH
MD ${pf}
&END EACH
&END CELL
&FORCES off
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END FORCES
&RESTART
BACKUP_COPIES 0
&EACH
MD ${pf}
&END EACH
&END RESTART
&RESTART_HISTORY
&EACH
MD 0
&END EACH
&END RESTART_HISTORY
&STRESS on
&EACH
MD ${pf}
&END EACH
&END STRESS
&STRUCTURE_DATA on
ANGLE 2 1 3
DISTANCE 1 2
DISTANCE 1 3
DISTANCE 2 3
&EACH
MD ${pf}
&END EACH
&END STRUCTURE_DATA
&TRAJECTORY on
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END TRAJECTORY
&VELOCITIES off
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END VELOCITIES
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Fist
STRESS_TENSOR analytical
&MM
@FFTYPE H2O/${model}
&POISSON
&EWALD
ALPHA 0.35
EWALD_TYPE SPME
GMAX 6*${na} 6*${nb} 6*${nc}
O_SPLINE 6
&END EWALD
&END POISSON
&PRINT
&DIPOLE off
&END DIPOLE
&FF_INFO on
SPLINE_DATA off
SPLINE_INFO on
&END FF_INFO
&PROGRAM_RUN_INFO
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&END MM
&PRINT
&PROGRAM_RUN_INFO
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&SUBSYS
&CELL
ABC [Angstrom] ${a} ${a} ${a}
MULTIPLE_UNIT_CELL ${na} ${nb} ${nc}
&END CELL
&COORD
UNIT Angstrom
OW 1.5800000000 1.5800000000 1.5800000000 H2O
HW 1.5800000000 1.5800000000 2.5800000000 H2O
HW 2.5228161427 1.5800000000 1.2466867524 H2O
&END COORD
&KIND OW
ELEMENT O
&END KIND
&KIND HW
ELEMENT H
&END KIND
&TOPOLOGY
MULTIPLE_UNIT_CELL ${na} ${nb} ${nc}
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL

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tests/Fist/regtest-water/H2O-SPCE-6x6x6.inp Normal file
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# Cubic cell with 6*6*6 = 216 H2O molecules
@SET model SPCE
@SET doh 1.000000000
@SET dhh 1.632980862
@SET a 3.16
@SET na 6
@SET nb 6
@SET nc 6
@SET nh2o ${na}x${nb}x${nc}
@SET pf 10
&GLOBAL
PRINT_LEVEL medium
PROJECT H2O-${model}-${nh2o}
RUN_TYPE MD
&END GLOBAL
&MOTION
&CONSTRAINT
&G3X3
ATOMS 1 2 3
DISTANCES [Angstrom] ${doh} ${doh} ${dhh}
MOLNAME H2O
&END G3X3
&END CONSTRAINT
&MD
ENSEMBLE NpT_i
STEPS 50
TEMPERATURE [K] 300.0
TEMP_KIND on
TIMESTEP [fs] 0.5
&BAROSTAT
PRESSURE [bar] 1.0
TIMECON [fs] 1000.0
&PRINT
&ENERGY
&EACH
MD ${pf}
&END EACH
&END ENERGY
&END PRINT
&END BAROSTAT
&PRINT
&CENTER_OF_MASS on
&EACH
MD ${pf}
&END EACH
&END CENTER_OF_MASS
&ENERGY on
&EACH
MD ${pf}
&END EACH
&END ENERGY
&PROGRAM_RUN_INFO on
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&TEMP_KIND on
&EACH
MD ${pf}
&END EACH
&END TEMP_KIND
&END PRINT
&THERMOSTAT
REGION global
TYPE CSVR
&CSVR
TIMECON [fs] 100.0
&END CSVR
&END THERMOSTAT
&END MD
&PRINT
&CELL on
&EACH
MD ${pf}
&END EACH
&END CELL
&FORCES off
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END FORCES
&RESTART
BACKUP_COPIES 0
&EACH
MD ${pf}
&END EACH
&END RESTART
&RESTART_HISTORY
&EACH
MD 0
&END EACH
&END RESTART_HISTORY
&STRESS on
&EACH
MD ${pf}
&END EACH
&END STRESS
&STRUCTURE_DATA on
ANGLE 2 1 3
DISTANCE 1 2
DISTANCE 1 3
DISTANCE 2 3
&EACH
MD ${pf}
&END EACH
&END STRUCTURE_DATA
&TRAJECTORY on
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END TRAJECTORY
&VELOCITIES off
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END VELOCITIES
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Fist
STRESS_TENSOR analytical
&MM
@FFTYPE H2O/${model}
&POISSON
&EWALD
ALPHA 0.35
EWALD_TYPE SPME
GMAX 6*${na} 6*${nb} 6*${nc}
O_SPLINE 6
&END EWALD
&END POISSON
&PRINT
&DIPOLE off
&END DIPOLE
&FF_INFO on
SPLINE_DATA off
SPLINE_INFO on
&END FF_INFO
&PROGRAM_RUN_INFO
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&END MM
&PRINT
&PROGRAM_RUN_INFO
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&SUBSYS
&CELL
ABC [Angstrom] ${a} ${a} ${a}
MULTIPLE_UNIT_CELL ${na} ${nb} ${nc}
&END CELL
&COORD
UNIT Angstrom
OW 1.5800000000 1.5800000000 1.5800000000 H2O
HW 1.5800000000 1.5800000000 2.5800000000 H2O
HW 2.5228161427 1.5800000000 1.2466867524 H2O
&END COORD
&KIND OW
ELEMENT O
&END KIND
&KIND HW
ELEMENT H
&END KIND
&TOPOLOGY
MULTIPLE_UNIT_CELL ${na} ${nb} ${nc}
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL

179
tests/Fist/regtest-water/H2O-TIP3P-6x6x6.inp Normal file
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# Cubic cell with 6*6*6 = 216 H2O molecules
@SET model TIP3P
@SET doh 0.9572000000
@SET dhh 1.5139006545
@SET a 3.16
@SET na 6
@SET nb 6
@SET nc 6
@SET nh2o ${na}x${nb}x${nc}
@SET pf 10
&GLOBAL
PRINT_LEVEL medium
PROJECT H2O-${model}-${nh2o}
RUN_TYPE MD
&END GLOBAL
&MOTION
&CONSTRAINT
&G3X3
ATOMS 1 2 3
DISTANCES [Angstrom] ${doh} ${doh} ${dhh}
MOLNAME H2O
&END G3X3
&END CONSTRAINT
&MD
ENSEMBLE NpT_i
STEPS 50
TEMPERATURE [K] 300.0
TEMP_KIND on
TIMESTEP [fs] 0.5
&BAROSTAT
PRESSURE [bar] 1.0
TIMECON [fs] 1000.0
&PRINT
&ENERGY
&EACH
MD ${pf}
&END EACH
&END ENERGY
&END PRINT
&END BAROSTAT
&PRINT
&CENTER_OF_MASS on
&EACH
MD ${pf}
&END EACH
&END CENTER_OF_MASS
&ENERGY on
&EACH
MD ${pf}
&END EACH
&END ENERGY
&PROGRAM_RUN_INFO on
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&TEMP_KIND on
&EACH
MD ${pf}
&END EACH
&END TEMP_KIND
&END PRINT
&THERMOSTAT
REGION global
TYPE CSVR
&CSVR
TIMECON [fs] 100.0
&END CSVR
&END THERMOSTAT
&END MD
&PRINT
&CELL on
&EACH
MD ${pf}
&END EACH
&END CELL
&FORCES off
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END FORCES
&RESTART
BACKUP_COPIES 0
&EACH
MD ${pf}
&END EACH
&END RESTART
&RESTART_HISTORY
&EACH
MD 0
&END EACH
&END RESTART_HISTORY
&STRESS on
&EACH
MD ${pf}
&END EACH
&END STRESS
&STRUCTURE_DATA on
ANGLE 2 1 3
DISTANCE 1 2
DISTANCE 1 3
DISTANCE 2 3
&EACH
MD ${pf}
&END EACH
&END STRUCTURE_DATA
&TRAJECTORY on
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END TRAJECTORY
&VELOCITIES off
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END VELOCITIES
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Fist
STRESS_TENSOR analytical
&MM
@FFTYPE H2O/${model}
&POISSON
&EWALD
ALPHA 0.35
EWALD_TYPE SPME
GMAX 6*${na} 6*${nb} 6*${nc}
O_SPLINE 6
&END EWALD
&END POISSON
&PRINT
&DIPOLE off
&END DIPOLE
&FF_INFO on
SPLINE_DATA off
SPLINE_INFO on
&END FF_INFO
&PROGRAM_RUN_INFO
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&END MM
&PRINT
&PROGRAM_RUN_INFO
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&SUBSYS
&CELL
ABC [Angstrom] ${a} ${a} ${a}
MULTIPLE_UNIT_CELL ${na} ${nb} ${nc}
&END CELL
&COORD
UNIT Angstrom
OW 1.5800000000 1.5800000000 1.5800000000 H2O
HW 1.5800000000 1.5800000000 2.5372000000 H2O
HW 2.5066272065 1.5800000000 1.3400127916 H2O
&END COORD
&KIND OW
ELEMENT O
&END KIND
&KIND HW
ELEMENT H
&END KIND
&TOPOLOGY
MULTIPLE_UNIT_CELL ${na} ${nb} ${nc}
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL

170
tests/Fist/regtest-water/H2O-TIP3P_FLEXIBLE-6x6x6.inp Normal file
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# Cubic cell with 6*6*6 = 216 H2O molecules
@SET model TIP3P_FLEXIBLE
@SET a 3.16
@SET na 6
@SET nb 6
@SET nc 6
@SET nh2o ${na}x${nb}x${nc}
@SET pf 10
&GLOBAL
PRINT_LEVEL medium
PROJECT H2O-${model}-${nh2o}
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NpT_i
STEPS 50
TEMPERATURE [K] 300.0
TEMP_KIND on
TIMESTEP [fs] 0.5
&BAROSTAT
PRESSURE [bar] 1.0
TIMECON [fs] 1000.0
&PRINT
&ENERGY
&EACH
MD ${pf}
&END EACH
&END ENERGY
&END PRINT
&END BAROSTAT
&PRINT
&CENTER_OF_MASS on
&EACH
MD ${pf}
&END EACH
&END CENTER_OF_MASS
&ENERGY on
&EACH
MD ${pf}
&END EACH
&END ENERGY
&PROGRAM_RUN_INFO on
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&TEMP_KIND on
&EACH
MD ${pf}
&END EACH
&END TEMP_KIND
&END PRINT
&THERMOSTAT
REGION global
TYPE CSVR
&CSVR
TIMECON [fs] 100.0
&END CSVR
&END THERMOSTAT
&END MD
&PRINT
&CELL on
&EACH
MD ${pf}
&END EACH
&END CELL
&FORCES off
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END FORCES
&RESTART
BACKUP_COPIES 0
&EACH
MD ${pf}
&END EACH
&END RESTART
&RESTART_HISTORY
&EACH
MD 0
&END EACH
&END RESTART_HISTORY
&STRESS on
&EACH
MD ${pf}
&END EACH
&END STRESS
&STRUCTURE_DATA on
ANGLE 2 1 3
DISTANCE 1 2
DISTANCE 1 3
DISTANCE 2 3
&EACH
MD ${pf}
&END EACH
&END STRUCTURE_DATA
&TRAJECTORY on
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END TRAJECTORY
&VELOCITIES off
FORMAT xyz
&EACH
MD ${pf}
&END EACH
&END VELOCITIES
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Fist
STRESS_TENSOR analytical
&MM
@FFTYPE H2O/${model}
&POISSON
&EWALD
ALPHA 0.35
EWALD_TYPE SPME
GMAX 6*${na} 6*${nb} 6*${nc}
O_SPLINE 6
&END EWALD
&END POISSON
&PRINT
&DIPOLE off
&END DIPOLE
&FF_INFO on
SPLINE_DATA off
SPLINE_INFO on
&END FF_INFO
&PROGRAM_RUN_INFO
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&END MM
&PRINT
&PROGRAM_RUN_INFO
&EACH
MD ${pf}
&END EACH
&END PROGRAM_RUN_INFO
&END PRINT
&SUBSYS
&CELL
ABC [Angstrom] ${a} ${a} ${a}
MULTIPLE_UNIT_CELL ${na} ${nb} ${nc}
&END CELL
&COORD
UNIT Angstrom
OW 1.5800000000 1.5800000000 1.5800000000 H2O
HW 1.5800000000 1.5800000000 2.5372000000 H2O
HW 2.5066272065 1.5800000000 1.3400127916 H2O
&END COORD
&KIND OW
ELEMENT O
&END KIND
&KIND HW
ELEMENT H
&END KIND
&TOPOLOGY
MULTIPLE_UNIT_CELL ${na} ${nb} ${nc}
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL

6
tests/Fist/regtest-water/TEST_FILES Normal file
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# Test common water models
H2O-SPC-6x6x6.inp 2 1.0E-12 -0.262569484903E+01
H2O-SPCE-6x6x6.inp 2 1.0E-12 -0.278895062813E+01
H2O-TIP3P-6x6x6.inp 2 1.0E-12 -0.270534423425E+01
H2O-TIP3P_FLEXIBLE-6x6x6.inp 2 1.0E-12 -0.263573237268E+01
#EOF

1
tests/TEST_DIRS
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@ -3,6 +3,7 @@
# Directories have been reordered according the execution time needed for a gfortran pdbg run using 2 MPI tasks
# in case a new directory is added just add it at the top of the list..
# the order will be regularly checked and modified...
Fist/regtest-water
QS/regtest-ecp libgrpp
QS/regtest-ecp-2 libgrpp
QS/regtest-as-3 libint mpiranks%2==0