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This commit is contained in:
Tom Swinburne
2020-04-14 21:21:22 +02:00
parent 6cbd61d929
commit b8d6de2bdc
4 changed files with 22 additions and 1447 deletions
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12
examples/USER/pafi/README
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@ -17,9 +17,15 @@ Physical Review Letters 276, 1 2018
Also see https://github.com/tomswinburne/pafi/ for PAFI++ code which uses the USER-PAFI package when loading LAMMPS as a C++ library
To run example:
To compile:
mpirun -np NUMPROCS lmp_machine < pafi.lammps
make yes-user-pafi # for PAFI
make yes-manybody # for EAM potential
make machine mode=lib # for library version (machine= e.g. mpi)
make machine # for binary (machine= e.g. mpi)
where NUMPROCS = # of procs and lmp_machine = e.g. lmp_mpi
To run the example from this folder:
```
mpirun -np NPROCS /path/to/lammps/src/lmp_machine < pafi.lammps
```

44
examples/USER/pafi/binary/pafi.lammps
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@ -1,44 +0,0 @@
units metal
atom_style atomic
atom_modify map array sort 0 0.0
neigh_modify every 2 delay 10 check yes page 1000000 one 100000
## read in path data using fix property/atom
fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
read_data test.dat fix pa NULL PafiPath
run 0
## EAM potential
pair_style eam/fs
pair_coeff * * ../Fe.eam.fs Fe
mass * 55.85
thermo 100
compute pe all pe
variable pe equal pe
run 0
print "energy=${pe}"
## compute property/atom to access relevant fields
compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
run 0
## fix name group-id hp compute-id temperature damp seed overdamped 0/1 com 0/1
fix hp all hp pa 400.0 0.1 234 overdamped 1 com 1
run 1000
## minimize under same constraint (temperature effectively zero)
min_style fire
minimize 0 0 1000 1000
print "energy=${pe}"
## minimize without constraint
unfix hp
minimize 0 0 1000 1000
print "energy=${pe}"

1391
examples/USER/pafi/binary/test.dat
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22
examples/USER/pafi/pafi.lammps
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@ -2,10 +2,6 @@ units metal
atom_style atomic
atom_modify map array sort 0 0.0
neigh_modify every 2 delay 10 check yes page 1000000 one 100000
## read in path data using fix property/atom
fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
read_data test.dat fix pa NULL PafiPath
@ -13,7 +9,7 @@ run 0
## EAM potential
pair_style eam/fs
pair_coeff * * Fe.eam.fs Fe
pair_coeff * * ../Fe.eam.fs Fe
mass * 55.85
thermo 100
@ -22,23 +18,31 @@ variable pe equal pe
run 0
print "energy=${pe}"
## compute property/atom to access 9 fields
## compute property/atom to access relevant fields
compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
run 0
## fix name group-id hp compute-id temperature damp seed overdamped 0/1 com 0/1
fix hp all hp pa 400.0 0.1 234 overdamped 1 com 1
fix hp all hp pa 400.0 0.1 434 overdamped 1 com 1
run 0
variable dn equal f_hp[4]*f_hp[4] # should be zero
fix af all ave/time 1 1000 1000 f_hp[1] f_hp[2] f_hp[3] v_dn
variable adn equal f_af[4] # should be zero
variable apf equal f_af[1]
run 1000
## minimize under same constraint
print "Squared displacement normal to hyperplane = ${adn} A^2"
print "average projected force = ${apf} eV/A"
## minimize under same constraint (temperature effectively zero)
min_style fire
minimize 0 0 1000 1000
print "energy=${pe}"
## minimize without constraint
unfix af
unfix hp
minimize 0 0 1000 1000
print "energy=${pe}"