more debugging and examples with NWChem
This commit is contained in:
Steve Plimpton
@ -106,14 +106,52 @@ Step 4: run the 2-water QMMM problem for a few steps
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% cd ~/lammps/examples/QUANTUM/NWChem
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% cd ~/lammps/examples/QUANTUM/NWChem
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lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.nwchem.qmmm.tcp.1 -in in.water.nwchem.qmmm &
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lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water,qmmm.tcp.1 -in in.water.qmmm &
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python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.water.nw water.dimer.nw log.water.pwdft.qmmm.tcp.1
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python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.water.nw water.dimer.nw log.water.pwdft.qmmm.tcp.1
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# Run with MPI: 1 proc each
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# Run with MPI: 1 proc each
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mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.nwchem.qmmm.mpi.1 -in in.water.nwchem.qmmm : -np 1 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.water.nw water.dimer.nw log.water.pwdft.qmmm.mpi.1
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mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.qmmm.mpi.1 -in in.water.qmmm : -np 1 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.water.nw water.dimer.nw log.water.pwdft.qmmm.mpi.1
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# Run in plugin mode: 1 proc
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# Run in plugin mode: 1 proc
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lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/work_qm" -log log.water.nwchem.qmmm.plugin.1 -in in.water.nwchem.qmmm.plugin
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lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.water.qmmm.plugin.1 -in in.water.qmmm.plugin
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---------------------------------
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---------------------------------
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Step 5: run the zeolite/methane QMMM problem for a few steps
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% cd ~/lammps/examples/QUANTUM/NWChem
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lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.zeolite.qmmm.tcp.1 -in in.zeolite.qmmm &
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python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.tcp.1
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# Run with MPI: 1 proc each
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mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.zeolite.qmmm.mpi.1 -in in.zeolite.qmmm : -np 1 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.mpi.1
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# Run in plugin mode: 1 proc
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lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.zeolite.qmmm.plugin.1 -in in.zeolite.qmmm.plugin
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---------------------------------
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---------------------------------
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Step 6: run multiple W geometries
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% cd ~/lammps/examples/QUANTUM/NWChem
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lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.series.tcp.1 -in in.series &
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python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.w.nw w.nw log.series.pwdft.tcp.1
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# Run with MPI: 1 proc each
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mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.series.mpi.1 -in in.series : -np 1 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.w.nw w.nw log.series.pwdft.mpi.1
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# Run in plugin mode: 1 proc
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lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/examples/QUANTUM/NWChem" -log log.series.plugin.1 -in in.series.plugin
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12
examples/QUANTUM/NWChem/data.w.bcc
Normal file
12
examples/QUANTUM/NWChem/data.w.bcc
Normal file
@ -0,0 +1,12 @@
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LAMMPS data file from VASP file VASP/POSCAR_bcc
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2 atoms
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1 atom types
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0.0 3.1654062429393064 xlo xhi
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0.0 3.1654062429393064 ylo yhi
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0.0 3.1654062429393064 zlo zhi
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Atoms
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1 1 0 0 0
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2 1 1.5827031214696532 1.5827031214696532 1.5827031214696532
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29
examples/QUANTUM/NWChem/data.w.bcc_222
Normal file
29
examples/QUANTUM/NWChem/data.w.bcc_222
Normal file
@ -0,0 +1,29 @@
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LAMMPS data file from VASP file VASP/POSCAR_bcc_222
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18 atoms
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1 atom types
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0.0 8.9531208783704628 xlo xhi
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0.0 3.8768150619108339 ylo yhi
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0.0 45.534159244872015 zlo zhi
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2.2382802195926157 0 0 xy xz yz
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Atoms
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1 1 0 0 15
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2 1 6.7148406587778462 1.2922716873036106 15.913774073227765
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3 1 4.4765604391852314 2.5845433746072226 16.827548146455531
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4 1 11.191401097963077 3.876815061910833 17.741322219683298
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5 1 6.7148406587778471 1.2922716873036111 18.655096292911061
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6 1 4.4765604391852305 2.5845433746072222 19.568870366138828
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7 1 2.2382802195926152 3.876815061910833 20.482644439366592
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8 1 6.7148406587778453 1.2922716873036111 21.396418512594359
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9 1 4.4765604391852305 2.5845433746072222 22.310192585822122
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10 1 2.2382802195926148 3.8768150619108321 23.223966659049893
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11 1 6.7148406587778453 1.2922716873036102 24.137740732277656
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12 1 4.4765604391852305 2.5845433746072195 25.051514805505423
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13 1 2.2382802195926148 3.8768150619108321 25.965288878733183
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14 1 6.7148406587778444 1.2922716873036084 26.879062951960954
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15 1 4.4765604391852314 2.5845433746072204 27.792837025188717
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16 1 2.2382802195926139 3.8768150619108304 28.706611098416481
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17 1 6.7148406587778453 1.2922716873036102 29.620385171644248
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18 1 4.4765604391852269 2.5845433746072204 30.534159244872015
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14
examples/QUANTUM/NWChem/data.w.diamond
Normal file
14
examples/QUANTUM/NWChem/data.w.diamond
Normal file
@ -0,0 +1,14 @@
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LAMMPS data file from VASP file VASP/POSCAR_diamond
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4 atoms
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1 atom types
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0.0 2.8200563642280549 xlo xhi
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0.0 2.8200563642280549 ylo yhi
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0.0 3.9881619569478763 zlo zhi
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Atoms
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1 1 0 0 0
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2 1 1.4100281821140275 0 0.99704048923696909
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3 1 1.4100281821140275 1.4100281821140275 1.9940809784739382
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4 1 0 1.4100281821140275 2.991121467710907
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28
examples/QUANTUM/NWChem/data.w.fcc_001
Normal file
28
examples/QUANTUM/NWChem/data.w.fcc_001
Normal file
@ -0,0 +1,28 @@
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LAMMPS data file from VASP file VASP/POSCAR_fcc_001
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18 atoms
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1 atom types
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0.0 4.4765604391852305 xlo xhi
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0.0 4.4765604391852305 ylo yhi
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0.0 113.81190612996821 zlo zhi
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Atoms
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1 1 0 0 30
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2 1 2.2382802195926152 2.2382802195926152 33.165406242939305
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3 1 0 0 36.33081248587861
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4 1 2.2382802195926152 2.2382802195926152 39.496218728817922
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5 1 0 0 42.661624971757227
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6 1 2.2382802195926152 2.2382802195926152 45.827031214696532
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7 1 0 0 48.992437457635837
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8 1 2.2382802195926152 2.2382802195926152 52.157843700575143
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9 1 0 0 55.323249943514455
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10 1 2.2382802195926152 2.2382802195926152 58.488656186453753
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11 1 0 0 61.654062429393065
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12 1 2.2382802195926152 2.2382802195926152 64.819468672332363
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13 1 0 0 67.984874915271675
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14 1 2.2382802195926152 2.2382802195926152 71.150281158210987
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15 1 0 0 74.315687401150285
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16 1 2.2382802195926152 2.2382802195926152 77.481093644089597
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17 1 0 0 80.646499887028909
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18 1 2.2382802195926152 2.2382802195926152 83.811906129968207
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19
examples/QUANTUM/NWChem/data.w.sc_001
Normal file
19
examples/QUANTUM/NWChem/data.w.sc_001
Normal file
@ -0,0 +1,19 @@
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LAMMPS data file from VASP file VASP/POSCAR_sc_001
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9 atoms
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1 atom types
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0.0 2.5123845999742804 xlo xhi
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0.0 2.5123845999742804 ylo yhi
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0.0 50.099076799794247 zlo zhi
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Atoms
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1 1 0 0 15.000000000000002
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2 1 0 0 17.512384599974283
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3 1 0 0 20.024769199948562
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4 1 0 0 22.537153799922841
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5 1 0 0 25.049538399897123
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6 1 0 0 27.561922999871406
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7 1 0 0 30.074307599845682
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8 1 0 0 32.586692199819964
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9 1 0 0 35.099076799794247
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45
examples/QUANTUM/NWChem/data.water.mm
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45
examples/QUANTUM/NWChem/data.water.mm
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@ -0,0 +1,45 @@
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LAMMPS data file for water dimer in large box
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6 atoms
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4 bonds
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2 angles
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2 atom types
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1 bond types
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1 angle types
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-6.879301 6.879301 xlo xhi
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-6.879301 6.879301 ylo yhi
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-6.879301 6.879301 zlo zhi
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Masses
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1 15.99491
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2 1.008
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Bond Coeffs
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1 554.25 1.0
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Angle Coeffs
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1 47.744 109.4
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Atoms
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1 1 1 -0.8476 0.161560 -0.052912 0.033173
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2 1 2 0.4238 0.803054 0.369132 -0.511660
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3 1 2 0.4238 -0.325571 -0.669574 -0.488560
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4 2 1 -0.8476 0.021259 0.506771 2.831278
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5 2 2 0.4238 -0.721039 1.083100 2.758378
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6 2 2 0.4238 0.158220 0.181883 1.945696
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Bonds
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1 1 1 2
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2 1 1 3
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3 1 4 5
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4 1 4 6
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Angles
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1 1 2 1 3
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2 1 5 4 6
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114
examples/QUANTUM/NWChem/data.zeolite
Normal file
114
examples/QUANTUM/NWChem/data.zeolite
Normal file
@ -0,0 +1,114 @@
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LAMMPS data file for SiO2 zeolite with one methane moleclue
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77 atoms
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4 atom types
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4 bonds
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1 bond types
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6 angles
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1 angle types
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-5.9266 5.9926 xlo xhi
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-5.9266 5.9926 ylo yhi
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-5.9266 5.9926 zlo zhi
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Masses
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1 28.0855
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2 15.99491
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3 12.0
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4 1.008
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Atoms
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1 0 1 1.910418 0.00000 4.38651 2.18123
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2 0 1 1.910418 0.00000 -4.38651 2.18123
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3 0 1 1.910418 0.00000 4.38651 -2.18123
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4 0 1 1.910418 0.00000 -4.38651 -2.18123
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5 0 1 1.910418 2.18123 0.00000 4.38651
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6 0 1 1.910418 2.18123 0.00000 -4.38651
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7 0 1 1.910418 -2.18123 0.00000 4.38651
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8 0 1 1.910418 -2.18123 0.00000 -4.38651
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9 0 1 1.910418 4.38651 2.18123 0.00000
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10 0 1 1.910418 -4.38651 2.18123 0.00000
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11 0 1 1.910418 4.38651 -2.18123 0.00000
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12 0 1 1.910418 -4.38651 -2.18123 0.00000
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13 0 1 1.910418 4.38651 0.00000 -2.18123
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14 0 1 1.910418 -4.38651 0.00000 -2.18123
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15 0 1 1.910418 4.38651 0.00000 2.18123
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16 0 1 1.910418 -4.38651 0.00000 2.18123
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17 0 1 1.910418 0.00000 2.18123 -4.38651
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||||||
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18 0 1 1.910418 0.00000 2.18123 4.38651
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19 0 1 1.910418 0.00000 -2.18123 -4.38651
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20 0 1 1.910418 0.00000 -2.18123 4.38651
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21 0 1 1.910418 2.18123 4.38651 0.00000
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22 0 1 1.910418 2.18123 -4.38651 0.00000
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23 0 1 1.910418 -2.18123 4.38651 0.00000
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24 0 1 1.910418 -2.18123 -4.38651 0.00000
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25 0 2 -0.955209 0.00000 -5.92660 2.64860
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26 0 2 -0.955209 0.00000 -5.92660 -2.64860
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27 0 2 -0.955209 2.64860 0.00000 -5.92660
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28 0 2 -0.955209 -2.64860 0.00000 -5.92660
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29 0 2 -0.955209 -5.92660 2.64860 0.00000
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30 0 2 -0.955209 -5.92660 -2.64860 0.00000
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31 0 2 -0.955209 -5.92660 0.00000 -2.64860
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32 0 2 -0.955209 -5.92660 0.00000 2.64860
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33 0 2 -0.955209 0.00000 2.64860 -5.92660
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34 0 2 -0.955209 0.00000 -2.64860 -5.92660
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35 0 2 -0.955209 2.64860 -5.92660 0.00000
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36 0 2 -0.955209 -2.64860 -5.92660 0.00000
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37 0 2 -0.955209 0.00000 3.45272 3.45272
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38 0 2 -0.955209 0.00000 -3.45272 3.45272
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39 0 2 -0.955209 0.00000 3.45272 -3.45272
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40 0 2 -0.955209 0.00000 -3.45272 -3.45272
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41 0 2 -0.955209 3.45272 0.00000 3.45272
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42 0 2 -0.955209 3.45272 0.00000 -3.45272
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43 0 2 -0.955209 -3.45272 0.00000 3.45272
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44 0 2 -0.955209 -3.45272 0.00000 -3.45272
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45 0 2 -0.955209 3.45272 3.45272 0.00000
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46 0 2 -0.955209 -3.45272 3.45272 0.00000
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47 0 2 -0.955209 3.45272 -3.45272 0.00000
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48 0 2 -0.955209 -3.45272 -3.45272 0.00000
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49 0 2 -0.955209 1.28702 1.28702 4.12598
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50 0 2 -0.955209 -1.28702 -1.28702 4.12598
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51 0 2 -0.955209 -1.28702 1.28702 -4.12598
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52 0 2 -0.955209 1.28702 -1.28702 -4.12598
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53 0 2 -0.955209 4.12598 1.28702 1.28702
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54 0 2 -0.955209 4.12598 -1.28702 -1.28702
|
||||||
|
55 0 2 -0.955209 -4.12598 -1.28702 1.28702
|
||||||
|
56 0 2 -0.955209 -4.12598 1.28702 -1.28702
|
||||||
|
57 0 2 -0.955209 1.28702 4.12598 1.28702
|
||||||
|
58 0 2 -0.955209 -1.28702 4.12598 -1.28702
|
||||||
|
59 0 2 -0.955209 1.28702 -4.12598 -1.28702
|
||||||
|
60 0 2 -0.955209 -1.28702 -4.12598 1.28702
|
||||||
|
61 0 2 -0.955209 1.28702 1.28702 -4.12598
|
||||||
|
62 0 2 -0.955209 -1.28702 -1.28702 -4.12598
|
||||||
|
63 0 2 -0.955209 1.28702 -1.28702 4.12598
|
||||||
|
64 0 2 -0.955209 -1.28702 1.28702 4.12598
|
||||||
|
65 0 2 -0.955209 1.28702 4.12598 -1.28702
|
||||||
|
66 0 2 -0.955209 -1.28702 4.12598 1.28702
|
||||||
|
67 0 2 -0.955209 -1.28702 -4.12598 -1.28702
|
||||||
|
68 0 2 -0.955209 1.28702 -4.12598 1.28702
|
||||||
|
69 0 2 -0.955209 4.12598 1.28702 -1.28702
|
||||||
|
70 0 2 -0.955209 4.12598 -1.28702 1.28702
|
||||||
|
71 0 2 -0.955209 -4.12598 1.28702 1.28702
|
||||||
|
72 0 2 -0.955209 -4.12598 -1.28702 -1.28702
|
||||||
|
73 1 3 -0.66 0.00000 0.00000 0.00000
|
||||||
|
74 1 4 0.165 0.00000 -0.89000 -0.62930
|
||||||
|
75 1 4 0.165 0.00000 0.89000 -0.62930
|
||||||
|
76 1 4 0.165 -0.89000 0.00000 0.62930
|
||||||
|
77 1 4 0.165 0.89000 0.00000 0.62930
|
||||||
|
|
||||||
|
Bonds
|
||||||
|
|
||||||
|
1 1 73 74
|
||||||
|
2 1 73 75
|
||||||
|
3 1 73 76
|
||||||
|
4 1 73 77
|
||||||
|
|
||||||
|
Angles
|
||||||
|
|
||||||
|
1 1 74 73 75
|
||||||
|
2 1 74 73 76
|
||||||
|
3 1 74 73 77
|
||||||
|
4 1 75 73 76
|
||||||
|
5 1 75 73 77
|
||||||
|
6 1 76 73 77
|
||||||
36
examples/QUANTUM/NWChem/in.series
Normal file
36
examples/QUANTUM/NWChem/in.series
Normal file
@ -0,0 +1,36 @@
|
|||||||
|
# multiple W conformations with NWChem
|
||||||
|
|
||||||
|
variable datafile index data.w.bcc data.w.diamond
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label loop
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map yes
|
||||||
|
comm_modify cutoff 2.0
|
||||||
|
|
||||||
|
log log.series.${datafile}
|
||||||
|
|
||||||
|
read_data ${datafile}
|
||||||
|
|
||||||
|
mass 1 183.84
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm elements W connect no
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
|
||||||
|
dump 1 all custom 1 dump.series.${datafile} id x y z fx fy fz
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next datafile
|
||||||
|
|
||||||
|
jump SELF loop
|
||||||
|
|
||||||
|
mdi exit
|
||||||
34
examples/QUANTUM/NWChem/in.series.plugin
Normal file
34
examples/QUANTUM/NWChem/in.series.plugin
Normal file
@ -0,0 +1,34 @@
|
|||||||
|
# multiple W conformations with NWChem
|
||||||
|
|
||||||
|
variable datafile index data.w.bcc data.w.diamond
|
||||||
|
|
||||||
|
label loop
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map yes
|
||||||
|
comm_modify cutoff 2.0
|
||||||
|
|
||||||
|
log log.series.plugin.${datafile}
|
||||||
|
|
||||||
|
read_data ${datafile}
|
||||||
|
|
||||||
|
mass 1 183.84
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm elements W
|
||||||
|
fix_modify 1 energy yes
|
||||||
|
|
||||||
|
dump 1 all custom 1 dump.series.plugin.${datafile} id x y z fx fy fz
|
||||||
|
|
||||||
|
mdi plugin nwchem_mdi mdi "-role ENGINE -name LATTE -method LINK" &
|
||||||
|
extra "template.w.nw w.nw log.series.pwdft.plugin.1" &
|
||||||
|
command "run 0"
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next datafile
|
||||||
|
|
||||||
|
jump SELF loop
|
||||||
34
examples/QUANTUM/NWChem/in.w.many
Normal file
34
examples/QUANTUM/NWChem/in.w.many
Normal file
@ -0,0 +1,34 @@
|
|||||||
|
# many conformations with NWChem
|
||||||
|
|
||||||
|
variable datafiles file file.list.2
|
||||||
|
|
||||||
|
label loop
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map yes
|
||||||
|
comm_modify cutoff 2.0
|
||||||
|
|
||||||
|
log log.${datafiles}
|
||||||
|
|
||||||
|
read_data Wfiles/${datafiles}
|
||||||
|
|
||||||
|
mass 1 183.84
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 2 all nwchem template.w.nw ${datafiles}.nw &
|
||||||
|
log.pwdft.${datafiles} W
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
dump 1 all custom 1 dump.${datafiles} id x y z fx fy fz
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
next datafiles
|
||||||
|
jump SELF loop
|
||||||
46
examples/QUANTUM/NWChem/in.water.mm
Normal file
46
examples/QUANTUM/NWChem/in.water.mm
Normal file
@ -0,0 +1,46 @@
|
|||||||
|
# MM for water dimer
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
|
||||||
|
read_data data.water.mm
|
||||||
|
|
||||||
|
group mm molecule 1
|
||||||
|
group qm molecule 2
|
||||||
|
|
||||||
|
# pair style must define stand-alone short-range Coulombics
|
||||||
|
|
||||||
|
pair_style lj/cut/coul/cut 6.0
|
||||||
|
pair_coeff 1 1 0.13506 3.166
|
||||||
|
pair_coeff 2 2 0.0 1.0
|
||||||
|
|
||||||
|
#velocity all create 300.0 458732
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
compute 1 all pair/local dist
|
||||||
|
compute 2 all reduce max c_1
|
||||||
|
|
||||||
|
variable fxabs atom abs(fx)
|
||||||
|
variable fyabs atom abs(fy)
|
||||||
|
variable fzabs atom abs(fz)
|
||||||
|
variable qabs atom abs(q)
|
||||||
|
compute 3 all reduce max v_fxabs v_fyabs v_fzabs v_qabs
|
||||||
|
|
||||||
|
dump 1 all custom 1 dump.water.dimer.mm id x y z q fx fy fz
|
||||||
|
dump_modify 1 sort id format float "%20.16g"
|
||||||
|
|
||||||
|
timestep 1.0
|
||||||
|
|
||||||
|
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||||
|
pe etotal press c_2 c_3[*]
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 10
|
||||||
@ -6,7 +6,7 @@ atom_style full
|
|||||||
bond_style harmonic
|
bond_style harmonic
|
||||||
angle_style harmonic
|
angle_style harmonic
|
||||||
|
|
||||||
read_data data.water.nwchem.qmmm
|
read_data data.water.qmmm
|
||||||
|
|
||||||
# QM atoms are 1st water
|
# QM atoms are 1st water
|
||||||
# MM atoms are 2nd water
|
# MM atoms are 2nd water
|
||||||
@ -49,22 +49,11 @@ timestep 0.1
|
|||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
|
|
||||||
fix 2 qm mdi/qmmm potential elements 8 1 8 1
|
fix 2 qm mdi/qmmm potential elements O H O H
|
||||||
#fix 2 qm nwchem template.water.nw water.dimer2.nw &
|
|
||||||
# log.pwdft.water.dimer O H O H
|
|
||||||
fix_modify 2 energy yes
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||||
f_2 pe etotal press
|
f_2 pe etotal press
|
||||||
|
|
||||||
# convert dump file forces to Hartree/Bohr for comparison to NWChem
|
|
||||||
|
|
||||||
variable fx atom fx/1185.8
|
|
||||||
variable fy atom fy/1185.8
|
|
||||||
variable fz atom fz/1185.8
|
|
||||||
|
|
||||||
dump 1 all custom 1 dump.water.nwchem.qmmm id x y z q v_fx v_fy v_fz
|
|
||||||
dump_modify 1 sort id format float "%20.16g"
|
|
||||||
|
|
||||||
thermo 1
|
thermo 1
|
||||||
run 2
|
run 2
|
||||||
@ -6,7 +6,7 @@ atom_style full
|
|||||||
bond_style harmonic
|
bond_style harmonic
|
||||||
angle_style harmonic
|
angle_style harmonic
|
||||||
|
|
||||||
read_data data.water.nwchem.qmmm
|
read_data data.water.qmmm
|
||||||
|
|
||||||
# QM atoms are 1st water
|
# QM atoms are 1st water
|
||||||
# MM atoms are 2nd water
|
# MM atoms are 2nd water
|
||||||
@ -49,24 +49,13 @@ timestep 0.1
|
|||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
|
|
||||||
fix 2 qm mdi/qmmm potential elements 8 1 8 1
|
fix 2 qm mdi/qmmm potential elements O H O H
|
||||||
fix_modify 2 energy yes
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||||
f_2 pe etotal press
|
f_2 pe etotal press
|
||||||
|
|
||||||
# convert dump file forces to Hartree/Bohr for comparison to NWChem
|
|
||||||
|
|
||||||
variable fx atom fx/1185.8
|
|
||||||
variable fy atom fy/1185.8
|
|
||||||
variable fz atom fz/1185.8
|
|
||||||
|
|
||||||
dump 1 all custom 1 dump.water.dimer.qmmm.plugin &
|
|
||||||
id x y z q v_fx v_fy v_fz
|
|
||||||
dump_modify 1 sort id format float "%20.16g"
|
|
||||||
|
|
||||||
thermo 1
|
thermo 1
|
||||||
|
|
||||||
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" &
|
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" &
|
||||||
extra "template.water.nw water.dimer.nw log.water.pwdft.qmmm.plugin.1" &
|
extra "template.water.nw water.dimer.nw log.water.pwdft.qmmm.plugin.1" &
|
||||||
command "run 2"
|
command "run 1"
|
||||||
116
examples/QUANTUM/NWChem/in.zeolite.mm
Normal file
116
examples/QUANTUM/NWChem/in.zeolite.mm
Normal file
@ -0,0 +1,116 @@
|
|||||||
|
# MM for SiO2 zeolite with one methane molecule
|
||||||
|
|
||||||
|
# CHIK potential
|
||||||
|
# EPL, Carre, Horbach, Ispas, Kob, 82, 17001 (2008)
|
||||||
|
# B = 1/rho
|
||||||
|
|
||||||
|
#q Si = 1.910418
|
||||||
|
#q O = -0.955209
|
||||||
|
#A OO = 659.595398 eV
|
||||||
|
#B OO = 2.590066 1/Ang
|
||||||
|
#C OO = 26.836679 eV-Ang^6
|
||||||
|
#A SiO = 27029.419922 eV
|
||||||
|
#B SiO = 5.158606 1/Ang
|
||||||
|
#C SiO = 148.099091 eV-Ang^6
|
||||||
|
#A SiSi = 3150.462646 eV
|
||||||
|
#B SiSi = 2.851451 1/Ang
|
||||||
|
#C SiSi = 626.7519553 eV-Ang^6
|
||||||
|
|
||||||
|
# LJ params for methane and O from Table 1
|
||||||
|
# Bhatia and Nicholson, J Phys Chem C, 2012, 116, 2344-2355.
|
||||||
|
|
||||||
|
#q C = -0.66
|
||||||
|
#Q H = 0.165
|
||||||
|
#sigma C = 0.34 nm
|
||||||
|
#sigma H = 0.265 nm
|
||||||
|
#sigma O = 0.28 nm
|
||||||
|
#eps/kB C = 55.082 K = 0.004745993 eV
|
||||||
|
#eps/kB H = 7.905 K = 0.000681113 eV
|
||||||
|
#eps/kB O = 492.7 K = 0.0424522 eV
|
||||||
|
|
||||||
|
# LJ params for silicon
|
||||||
|
#e-Journal of Surf Sci and Nanotech, Inui and Iwasaki, 15, 40-49 (2017)
|
||||||
|
|
||||||
|
#sigma Si = 3.826 Ang
|
||||||
|
#eps Si = 17.4 meV = 0.0174 eV
|
||||||
|
|
||||||
|
# C-H bond and methane angle params
|
||||||
|
|
||||||
|
#OPLS C-H bond k = 29.40 ev/Ang^2
|
||||||
|
#C-H bond r0 = 1.09 Angs
|
||||||
|
#methane angles = 109.5 degrees
|
||||||
|
#C-H angle k/kB = 2000 K/rad^2
|
||||||
|
|
||||||
|
# conversions
|
||||||
|
|
||||||
|
#1 eV = 11606 K
|
||||||
|
#1 eV = 23.0609 kcal/mole
|
||||||
|
#1 kcal/mole = 503.2761 K
|
||||||
|
#1 kcal = 4.814 kJoule
|
||||||
|
|
||||||
|
# -------------------------
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
|
||||||
|
read_data data.zeolite
|
||||||
|
|
||||||
|
group mm type 1 2
|
||||||
|
group qm type 3 4
|
||||||
|
|
||||||
|
# pair style must define stand-alone short-range Coulombics
|
||||||
|
# arithmetic mixing
|
||||||
|
|
||||||
|
pair_style hybrid/overlay buck 6.5 lj/cut 6.5 coul/cut 6.5
|
||||||
|
|
||||||
|
pair_coeff 1 1 buck 3150.462646 0.35032282 626.7519553
|
||||||
|
pair_coeff 2 2 buck 659.595398 0.38609055 26.836679
|
||||||
|
pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
|
||||||
|
pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
|
||||||
|
pair_coeff 1 3 lj/cut 0.009087 3.613
|
||||||
|
pair_coeff 1 4 lj/cut 0.00344258 3.238
|
||||||
|
pair_coeff 2 3 lj/cut 0.01419429 3.1
|
||||||
|
pair_coeff 2 4 lj/cut 0.00537724 2.725
|
||||||
|
pair_coeff 3 3 lj/cut 0.004746 3.4
|
||||||
|
pair_coeff 4 4 lj/cut 0.00068111 2.65
|
||||||
|
pair_coeff * * coul/cut
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 29.40 1.09
|
||||||
|
|
||||||
|
angle_style harmonic
|
||||||
|
angle_coeff 1 0.172325 109.5
|
||||||
|
|
||||||
|
#velocity all create 300.0 458732
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
# dynamic or frozen zeolite
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
#fix 1 qm nve
|
||||||
|
|
||||||
|
compute 1 all pair/local dist
|
||||||
|
compute 2 all reduce max c_1
|
||||||
|
|
||||||
|
variable fxabs atom abs(fx)
|
||||||
|
variable fyabs atom abs(fy)
|
||||||
|
variable fzabs atom abs(fz)
|
||||||
|
variable qabs atom abs(q)
|
||||||
|
compute 3 all reduce max v_fxabs v_fyabs v_fzabs v_qabs
|
||||||
|
|
||||||
|
dump 1 all custom 1 dump.zeolite.mm id x y z q fx fy fz
|
||||||
|
dump_modify 1 sort id format float "%20.16g"
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||||
|
pe etotal press c_2 c_3[*]
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 3
|
||||||
70
examples/QUANTUM/NWChem/in.zeolite.qmmm
Normal file
70
examples/QUANTUM/NWChem/in.zeolite.qmmm
Normal file
@ -0,0 +1,70 @@
|
|||||||
|
# QMMM for SiO2 zeolite with one methane molecule
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
|
||||||
|
read_data data.zeolite
|
||||||
|
|
||||||
|
# MM atoms are Si,O
|
||||||
|
# QM atoms are C,H
|
||||||
|
|
||||||
|
group mm type 1 2
|
||||||
|
group qm type 3 4
|
||||||
|
|
||||||
|
# pair style must define stand-alone short-range Coulombics
|
||||||
|
# must specify mixing explicitly b/c hybrid/overlay
|
||||||
|
# MM Si,O = types 1,2
|
||||||
|
# QM C,H = types 3,4
|
||||||
|
# MM Si,O atoms do not LJ interact with each other (just via Buckingham)
|
||||||
|
# QM C,H atoms do not LJ interact with each other
|
||||||
|
# MM Si,O and QM C,H do LJ interact with each other
|
||||||
|
|
||||||
|
pair_style hybrid/overlay buck 6.5 lj/cut 6.5 coul/cut 6.5
|
||||||
|
|
||||||
|
pair_coeff 1 1 buck 3150.462646 0.35032282 626.7519553
|
||||||
|
pair_coeff 2 2 buck 659.595398 0.38609055 26.836679
|
||||||
|
pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
|
||||||
|
|
||||||
|
pair_coeff 1 3 lj/cut 0.09087 3.613
|
||||||
|
pair_coeff 1 4 lj/cut 0.0344258 3.238
|
||||||
|
pair_coeff 2 3 lj/cut 0.1419429 3.1
|
||||||
|
pair_coeff 2 4 lj/cut 0.035857762359063315 1.932779
|
||||||
|
|
||||||
|
pair_coeff 3 3 lj/cut 0.0 3.4
|
||||||
|
pair_coeff 4 4 lj/cut 0.0 2.65
|
||||||
|
pair_coeff * * coul/cut
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 29.40 1.09
|
||||||
|
|
||||||
|
angle_style harmonic
|
||||||
|
angle_coeff 1 0.172325 109.5
|
||||||
|
|
||||||
|
# remove bonds/angles in QM methane molecule
|
||||||
|
|
||||||
|
delete_bonds qm multi remove special
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
velocity all create 300.0 458732
|
||||||
|
|
||||||
|
# QMMM dynamics with small timestep
|
||||||
|
# dynamic or frozen zeolite
|
||||||
|
|
||||||
|
#fix 1 all nve
|
||||||
|
fix 1 qm nve
|
||||||
|
|
||||||
|
fix 2 qm mdi/qmmm potential elements Si O C H
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
|
||||||
|
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||||
|
f_2 pe etotal press
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 2
|
||||||
72
examples/QUANTUM/NWChem/in.zeolite.qmmm.plugin
Normal file
72
examples/QUANTUM/NWChem/in.zeolite.qmmm.plugin
Normal file
@ -0,0 +1,72 @@
|
|||||||
|
# QMMM for SiO2 zeolite with one methane molecule
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style full
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
|
||||||
|
read_data data.zeolite
|
||||||
|
|
||||||
|
# MM atoms are Si,O
|
||||||
|
# QM atoms are C,H
|
||||||
|
|
||||||
|
group mm type 1 2
|
||||||
|
group qm type 3 4
|
||||||
|
|
||||||
|
# pair style must define stand-alone short-range Coulombics
|
||||||
|
# must specify mixing explicitly b/c hybrid/overlay
|
||||||
|
# MM Si,O = types 1,2
|
||||||
|
# QM C,H = types 3,4
|
||||||
|
# MM Si,O atoms do not LJ interact with each other (just via Buckingham)
|
||||||
|
# QM C,H atoms do not LJ interact with each other
|
||||||
|
# MM Si,O and QM C,H do LJ interact with each other
|
||||||
|
|
||||||
|
pair_style hybrid/overlay buck 6.5 lj/cut 6.5 coul/cut 6.5
|
||||||
|
|
||||||
|
pair_coeff 1 1 buck 3150.462646 0.35032282 626.7519553
|
||||||
|
pair_coeff 2 2 buck 659.595398 0.38609055 26.836679
|
||||||
|
pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
|
||||||
|
|
||||||
|
pair_coeff 1 3 lj/cut 0.09087 3.613
|
||||||
|
pair_coeff 1 4 lj/cut 0.0344258 3.238
|
||||||
|
pair_coeff 2 3 lj/cut 0.1419429 3.1
|
||||||
|
pair_coeff 2 4 lj/cut 0.035857762359063315 1.932779 # same as water dimer
|
||||||
|
|
||||||
|
pair_coeff 3 3 lj/cut 0.0 3.4
|
||||||
|
pair_coeff 4 4 lj/cut 0.0 2.65
|
||||||
|
pair_coeff * * coul/cut
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 29.40 1.09
|
||||||
|
|
||||||
|
angle_style harmonic
|
||||||
|
angle_coeff 1 0.172325 109.5
|
||||||
|
|
||||||
|
# remove bonds/angles in QM methane molecule
|
||||||
|
|
||||||
|
delete_bonds qm multi remove special
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
velocity all create 300.0 458732
|
||||||
|
|
||||||
|
# QMMM dynamics with small timestep
|
||||||
|
# dynamic or frozen zeolite
|
||||||
|
|
||||||
|
#fix 1 all nve
|
||||||
|
fix 1 qm nve
|
||||||
|
|
||||||
|
fix 2 qm mdi/qmmm potential elements Si O C H
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
|
||||||
|
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||||
|
f_2 pe etotal press
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" &
|
||||||
|
extra "template.methane.nw methane.nw log.zeolite.pwdft.qmmm.plugin.1" &
|
||||||
|
command "run 2"
|
||||||
@ -493,9 +493,9 @@ def evaluate():
|
|||||||
qm_pe = c_qm_pe.value
|
qm_pe = c_qm_pe.value
|
||||||
time2 = time.time()
|
time2 = time.time()
|
||||||
print("DONE QMMM minimizer",nwerr,time2-time1)
|
print("DONE QMMM minimizer",nwerr,time2-time1)
|
||||||
print("PE",qm_pe)
|
#print("PE",qm_pe)
|
||||||
print("FORCE",qm_forces)
|
#print("FORCE",qm_forces)
|
||||||
print("CHARGES",qm_charges)
|
#print("CHARGES",qm_charges)
|
||||||
|
|
||||||
# AIMD with only QM atoms
|
# AIMD with only QM atoms
|
||||||
|
|
||||||
|
|||||||
17
examples/QUANTUM/NWChem/template.methane.nw
Normal file
17
examples/QUANTUM/NWChem/template.methane.nw
Normal file
@ -0,0 +1,17 @@
|
|||||||
|
Title "LAMMPS wrapping of PWDFT"
|
||||||
|
|
||||||
|
memory 1900 mb
|
||||||
|
|
||||||
|
echo
|
||||||
|
|
||||||
|
GEOMINSERT
|
||||||
|
|
||||||
|
nwpw
|
||||||
|
xc pbe
|
||||||
|
cutoff 30.0
|
||||||
|
2d-hcurve
|
||||||
|
tolerances 1.0e-9 1.0-9
|
||||||
|
apc on
|
||||||
|
end
|
||||||
|
|
||||||
|
task pspw gradient
|
||||||
16
examples/QUANTUM/NWChem/template.w.nw
Normal file
16
examples/QUANTUM/NWChem/template.w.nw
Normal file
@ -0,0 +1,16 @@
|
|||||||
|
Title "LAMMPS wrapping of PWDFT"
|
||||||
|
|
||||||
|
memory 1900 mb
|
||||||
|
|
||||||
|
echo
|
||||||
|
|
||||||
|
GEOMINSERT
|
||||||
|
|
||||||
|
nwpw
|
||||||
|
2d-hcurve
|
||||||
|
initialize_wavefunction on
|
||||||
|
cutoff 10.0
|
||||||
|
xc pbe
|
||||||
|
end
|
||||||
|
|
||||||
|
task pspw gradient
|
||||||
Reference in New Issue
Block a user