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new examples and debugging code changes

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This commit is contained in:
Steve Plimpton
2022-06-14 17:29:01 -06:00
parent 34863c6c97
commit a5745d925a
19 changed files with 507 additions and 81 deletions
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148
examples/mdi/README
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@ -50,7 +50,7 @@ changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
Run the entire calculation with a single instance of LAMMPS by itself Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI results should be identical to running this example with MDI
% lmp_mpi < in.aimd.alone % lmp_mpi -log log.aimd.alone < in.aimd.alone
With MDI, the thermo output of the driver should match the thermo With MDI, the thermo output of the driver should match the thermo
output of the in.aimd.alone script. output of the in.aimd.alone script.
@ -59,41 +59,157 @@ output of the in.aimd.alone script.
Run with TCP: 1 proc each Run with TCP: 1 proc each
% lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver % lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver
% lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine % lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine
--- ---
Run with TCP: 3 procs + 4 procs Run with TCP: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver % mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver
% mpirun -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine % mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine
--- ---
Run with MPI: 1 proc each Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine % mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine
--- ---
Run with MPI: 3 procs + 4 procs Run with MPI: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine % mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine
--- ---
Run in plugin mode: 1 proc Run in plugin mode: 1 proc
% lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin % lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
--- ---
Run in plugin mode: 3 procs Run in plugin mode: 3 procs
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin % mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
-------------------------------------------------
-------------------------------------------------
* Example #1b = run LAMMPS, compute QM forces on snapshots from a long run
Two instances of LAMMPS operate as a driver and engine
As an engine, LAMMPS is a surrogate for a quantum code
---
Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI
% lmp_mpi -log log.snapshot.alone < in.snapshot.alone
With MDI, the thermo output of the driver should match the thermo
output of the in.snapshot.alone script. Likewise the dump file written
by the driver should match dump.snapshot.alone.
---
Run with TCP: 1 proc each
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver
% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine
---
Run with TCP: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver
% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine
---
Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine
---
Run with MPI: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine
---
Run in plugin mode: 1 proc
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin
---
Run in plugin mode: 3 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin
-------------------------------------------------
-------------------------------------------------
* Example #1c = run LAMMPS, compute QM forces on series of independent systems
Two instances of LAMMPS operate as a driver and engine
As an engine, LAMMPS is a surrogate for a quantum code
---
Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI
% lmp_mpi -log log.series.alone < in.series.alone
With MDI, the thermo output of the driver should match the thermo
output of the in.series.alone script. Likewise the dump files written
by the driver should match dump.series.alone files.
---
Run with TCP: 1 proc each
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver
% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine
---
Run with TCP: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver
% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine
---
Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine
---
Run with MPI: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine
---
Run in plugin mode: 1 proc
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin
---
Run in plugin mode: 3 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin
------------------------------------------------- -------------------------------------------------
------------------------------------------------- -------------------------------------------------
@ -134,7 +250,7 @@ Run with TCP: 1 proc each
% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" % python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
% lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence % lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python
--- ---
@ -142,31 +258,31 @@ Run with TCP: 2 proc + 4 procs
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" % mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence % mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python
--- ---
Run with MPI: 1 proc each Run with MPI: 1 proc each
% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence % mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence.python
--- ---
Run with MPI: 2 procs + 4 procs Run with MPI: 2 procs + 4 procs
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence % mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence -in in.sequence.python
--- ---
Run in plugin mode: 1 proc Run in plugin mode: 1 proc
% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence" % python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python
--- ---
Run in plugin mode: 3 procs Run in plugin mode: 3 procs
% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence" % mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python
------------------------------------------------- -------------------------------------------------
------------------------------------------------- -------------------------------------------------
@ -190,7 +306,7 @@ here:
Run the entire calculation with a single instance of LAMMPS by itself Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI results should be identical to running this example with MDI
% lmp_mpi < in.aimd.alone % lmp_mpi -log log.aimd.alone < in.aimd.alone
With MDI, the driver prints the QM and Total energies. These should With MDI, the driver prints the QM and Total energies. These should
match the PotEng and TotEng output of the in.aimd.alone script. match the PotEng and TotEng output of the in.aimd.alone script.

3
examples/mdi/in.aimd.driver
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@ -23,8 +23,7 @@ fix 1 all nve
# NPT # NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 #fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/aimd fix 2 all mdi/qm virial yes
fix_modify 2 energy yes virial yes
thermo_style custom step temp pe etotal press vol thermo_style custom step temp pe etotal press vol
thermo 1 thermo 1

5
examples/mdi/in.aimd.driver.plugin
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@ -23,12 +23,11 @@ fix 1 all nve
# NPT # NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 #fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/aimd fix 2 all mdi/qm virial yes
fix_modify 2 energy yes virial yes
thermo_style custom step temp pe etotal press vol thermo_style custom step temp pe etotal press vol
thermo 1 thermo 1
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" & mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
infile in.aimd.engine extra "-log log.aimd.engine.plugin" & infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
command "run 5" command "run 5"

9
examples/mdi/in.aimd.engine
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@ -1,16 +1,11 @@
# 3d Lennard-Jones melt - MDI engine script # 3d Lennard-Jones melt - MDI engine script
variable x index 5
variable y index 5
variable z index 5
units lj units lj
atom_style atomic atom_style atomic
lattice fcc 0.8442 lattice fcc 1.0
region box block 0 $x 0 $y 0 $z region box block 0 1 0 1 0 1
create_box 1 box create_box 1 box
create_atoms 1 box
mass 1 1.0 mass 1 1.0
pair_style lj/cut 2.5 pair_style lj/cut 2.5

0
examples/mdi/in.sequence → examples/mdi/in.sequence.python
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43
examples/mdi/in.series.alone Normal file
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@ -0,0 +1,43 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable ifile loop 3
variable rho index 0.7 0.8 0.9
label LOOP
units lj
atom_style atomic
lattice fcc ${rho}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
displace_atoms all random 0.1 0.1 0.1 48294
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
compute 1 all pressure NULL virial
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
run 0
write_dump all custom dump.series.alone.${ifile} &
id type x y z fx fy fz modify sort id
clear
next ifile
next rho
jump SELF LOOP

48
examples/mdi/in.series.driver Normal file
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@ -0,0 +1,48 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable ifile loop 3
variable rho index 0.7 0.8 0.9
mdi start
label LOOP
units lj
atom_style atomic
lattice fcc ${rho}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
displace_atoms all random 0.1 0.1 0.1 48294
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes external yes
variable epress equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_epress f_1[1] f_1[2] f_1[3]
run 0
write_dump all custom dump.series.driver.${ifile} &
id type x y z f_1[1] f_1[2] f_1[3] modify sort id
# cannot do "clear" b/c will shutdown MDI engine
# have to
clear
next ifile
next rho
jump SELF LOOP
mdi stop

44
examples/mdi/in.series.driver.plugin Normal file
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@ -0,0 +1,44 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable ifile loop 3
variable rho index 0.7 0.8 0.9
label LOOP
units lj
atom_style atomic
lattice fcc ${rho}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
displace_atoms all random 0.1 0.1 0.1 48294
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes
variable epress equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_epress f_1[1] f_1[2] f_1[3]
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
infile in.series.engine &
extra "-log log.series.engine.plugin" &
command "run 0"
write_dump all custom dump.series.driver.${ifile} &
id type x y z f_1[1] f_1[2] f_1[3] modify sort id
clear
next ifile
next rho
jump SELF LOOP

17
examples/mdi/in.series.engine Normal file
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@ -0,0 +1,17 @@
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
region box block 0 1 0 1 0 1
create_box 1 box
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine

36
examples/mdi/in.snapshot.alone Normal file
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@ -0,0 +1,36 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
compute 1 all pressure NULL virial
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 500 dump.snapshot.alone &
id type x y z fx fy fz
dump_modify 1 sort id
run 1500

41
examples/mdi/in.snapshot.driver Normal file
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@ -0,0 +1,41 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 500 virial yes
compute 1 all pressure NULL virial
variable epress equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 500 dump.snapshot.driver &
id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
run 1500 pre no post no every 500 &
"print 'QM eng = $(f_2/atoms)'" &
"print 'QM virial = $(v_epress) $(f_2[1]) $(f_2[2]) $(f_2[3])'"

46
examples/mdi/in.snapshot.driver.plugin Normal file
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@ -0,0 +1,46 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 500 virial yes
compute 1 all pressure NULL virial
variable epress equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 500 dump.snapshot.driver &
id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
infile in.snapshot.engine &
extra "-log log.snapshot.engine.plugin" &
command """
run 1500 pre no post no every 500
"print 'QM eng = $(f_2/atoms)'"
"print 'QM virial = $(v_epress) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
"""

17
examples/mdi/in.snapshot.engine Normal file
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@ -0,0 +1,17 @@
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
region box block 0 1 0 1 0 1
create_box 1 box
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine

2
examples/mdi/sequence_driver.py
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@ -303,5 +303,5 @@ if not plugin:
if plugin: if plugin:
world = MPI.COMM_WORLD world = MPI.COMM_WORLD
plugin_args += " -mdi \"-role ENGINE -name lammps -method LINK\"" plugin_args += " -mdi \"-role ENGINE -name LMP -method LINK\""
mdi.MDI_Launch_plugin(plugin,plugin_args,world,perform_tasks,None) mdi.MDI_Launch_plugin(plugin,plugin_args,world,perform_tasks,None)

67
src/MDI/fix_mdi_qm.cpp
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@ -48,19 +48,20 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
virialflag = 0; virialflag = 0;
addflag = 1; addflag = 1;
every = 1; every = 1;
extflag = 0;
int iarg = 3; int iarg = 3;
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"virial") == 0) { if (strcmp(arg[iarg],"virial") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command"); if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command");
if (strcmp(arg[iarg],"yes") == 0) virialflag = 1; if (strcmp(arg[iarg+1],"yes") == 0) virialflag = 1;
else if (strcmp(arg[iarg],"no") == 0) virialflag = 0; else if (strcmp(arg[iarg+1],"no") == 0) virialflag = 0;
else error->all(FLERR,"Illegal fix mdi/qm command"); else error->all(FLERR,"Illegal fix mdi/qm command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"add") == 0) { } else if (strcmp(arg[iarg],"add") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command"); if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command");
if (strcmp(arg[iarg],"yes") == 0) addflag = 1; if (strcmp(arg[iarg+1],"yes") == 0) addflag = 1;
else if (strcmp(arg[iarg],"no") == 0) addflag = 0; else if (strcmp(arg[iarg+1],"no") == 0) addflag = 0;
else error->all(FLERR,"Illegal fix mdi/qm command"); else error->all(FLERR,"Illegal fix mdi/qm command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"every") == 0) { } else if (strcmp(arg[iarg],"every") == 0) {
@ -68,6 +69,12 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
every = utils::inumeric(FLERR,arg[iarg+1],false,lmp); every = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (every <= 0) error->all(FLERR,"Illegal fix mdi/qm command"); if (every <= 0) error->all(FLERR,"Illegal fix mdi/qm command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"external") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command");
if (strcmp(arg[iarg+1],"yes") == 0) extflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) extflag = 0;
else error->all(FLERR,"Illegal fix mdi/qm command");
iarg += 2;
} else error->all(FLERR,"Illegal fix mdi/qm command"); } else error->all(FLERR,"Illegal fix mdi/qm command");
} }
@ -77,10 +84,14 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
global_freq = every; global_freq = every;
extscalar = 1; extscalar = 1;
peratom_flag = 1;
size_peratom_cols = 3;
peratom_freq = every;
extvector = 0;
if (virialflag) { if (virialflag) {
vector_flag = 1; vector_flag = 1;
size_vector = 6; size_vector = 6;
extvector = 1;
} }
if (addflag) { if (addflag) {
@ -135,7 +146,7 @@ FixMDIQM::~FixMDIQM()
// send exit command to engine if it is a stand-alone code // send exit command to engine if it is a stand-alone code
// for plugin, this happens in MDIPlugin::plugin_wrapper() // for plugin, this happens in MDIPlugin::plugin_wrapper()
if (!plugin) { if (!plugin && !extflag) {
int ierr = MDI_Send_command("EXIT", mdicomm); int ierr = MDI_Send_command("EXIT", mdicomm);
if (ierr) error->all(FLERR, "MDI: EXIT command"); if (ierr) error->all(FLERR, "MDI: EXIT command");
} }
@ -169,6 +180,8 @@ void FixMDIQM::init()
// also initializes mdicomm // also initializes mdicomm
// set plugin = 0/1 for engine = stand-alone code vs plugin library // set plugin = 0/1 for engine = stand-alone code vs plugin library
if (!extflag) {
if (mdicomm == MDI_COMM_NULL) { if (mdicomm == MDI_COMM_NULL) {
MDI_Get_communicator(&mdicomm, 0); MDI_Get_communicator(&mdicomm, 0);
if (mdicomm == MDI_COMM_NULL) { if (mdicomm == MDI_COMM_NULL) {
@ -185,10 +198,17 @@ void FixMDIQM::init()
} }
} }
} else {
plugin = 0;
mdicomm = lmp->mdicomm;
}
// send natoms, atom types, and simulation box to engine // send natoms, atom types, and simulation box to engine
// this will trigger setup of a new system // this will trigger setup of a new system
// subsequent calls in post_force() will be for same system until new init() // subsequent calls in post_force() will be for same system until new init()
reallocate();
int ierr = MDI_Send_command(">NATOMS", mdicomm); int ierr = MDI_Send_command(">NATOMS", mdicomm);
if (ierr) error->all(FLERR, "MDI: >NATOMS command"); if (ierr) error->all(FLERR, "MDI: >NATOMS command");
int n = static_cast<int> (atom->natoms); int n = static_cast<int> (atom->natoms);
@ -293,31 +313,25 @@ void FixMDIQM::post_force(int vflag)
} }
// optionally request pressure tensor from MDI engine, convert to virial // optionally request pressure tensor from MDI engine, convert to virial
// divide by nprocs so each proc stores a portion
// MPI_Allreduce is performed in compute_vector()
// qm_virial = fix output for global QM virial // qm_virial = fix output for global QM virial
if (virialflag) { if (virialflag) {
double ptensor[6];
ierr = MDI_Send_command("<STRESS", mdicomm); ierr = MDI_Send_command("<STRESS", mdicomm);
if (ierr) error->all(FLERR, "MDI: <STRESS command"); if (ierr) error->all(FLERR, "MDI: <STRESS command");
ierr = MDI_Recv(ptensor, 6, MDI_DOUBLE, mdicomm); ierr = MDI_Recv(qm_virial, 6, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: <STRESS data"); if (ierr) error->all(FLERR, "MDI: <STRESS data");
MPI_Bcast(ptensor, 6, MPI_DOUBLE, 0, world); MPI_Bcast(qm_virial, 6, MPI_DOUBLE, 0, world);
double volume = domain->xprd * domain->yprd * domain->zprd; for (int i = 0; i < 6; i++)
for (int i = 0; i < 6; i++) { qm_virial[i] *= mdi2lmp_pressure;
ptensor[i] *= mdi2lmp_pressure;
qm_virial[i] = ptensor[i] * volume / force->nktv2p / nprocs;
}
sumflag = 0;
} }
// optionally set fix->virial // optionally set fix->virial
// divide by nprocs so each proc stores a portion
if (virialflag && addflag) { if (virialflag && addflag) {
for (int i = 0; i < 6; i++) for (int i = 0; i < 6; i++)
virial[i] = qm_virial[i]; virial[i] = qm_virial[i]/nprocs;
} }
} }
@ -343,14 +357,7 @@ double FixMDIQM::compute_scalar()
double FixMDIQM::compute_vector(int n) double FixMDIQM::compute_vector(int n)
{ {
// only sum across procs one time return qm_virial[n];
if (sumflag == 0) {
MPI_Allreduce(qm_virial, qm_virial_all, 6, MPI_DOUBLE, MPI_SUM, world);
sumflag = 1;
}
return qm_virial_all[n];
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -388,7 +395,8 @@ void FixMDIQM::reallocate()
void FixMDIQM::send_types() void FixMDIQM::send_types()
{ {
memset(ibuf1, 0, atom->natoms * sizeof(int)); int n = static_cast<int> (atom->natoms);
memset(ibuf1, 0, n * sizeof(int));
// use local atomID to index into ordered ibuf1 // use local atomID to index into ordered ibuf1
@ -402,10 +410,11 @@ void FixMDIQM::send_types()
ibuf1[index] = type[i]; ibuf1[index] = type[i];
} }
int n = static_cast<int> (atom->natoms);
MPI_Reduce(ibuf1, ibuf1all, n, MPI_INT, MPI_SUM, 0, world); MPI_Reduce(ibuf1, ibuf1all, n, MPI_INT, MPI_SUM, 0, world);
int ierr = MDI_Send(ibuf1all, n, MDI_INT, mdicomm); int ierr = MDI_Send_command(">TYPES", mdicomm);
if (ierr) error->all(FLERR, "MDI: >TYPES command");
ierr = MDI_Send(ibuf1all, n, MDI_INT, mdicomm);
if (ierr) error->all(FLERR, "MDI: >TYPES data"); if (ierr) error->all(FLERR, "MDI: >TYPES data");
} }

2
src/MDI/fix_mdi_qm.h
View File

@ -40,7 +40,7 @@ class FixMDIQM : public Fix {
private: private:
int nprocs; int nprocs;
int virialflag,addflag,every; int virialflag,addflag,extflag,every;
int plugin; int plugin;
int maxlocal; int maxlocal;
int sumflag; int sumflag;

22
src/MDI/mdi_command.cpp
View File

@ -31,8 +31,26 @@ void MDICommand::command(int narg, char **arg)
if (strcmp(arg[0], "engine") == 0) { if (strcmp(arg[0], "engine") == 0) {
MDIEngine(lmp, narg - 1, &arg[1]); MDIEngine(lmp, narg - 1, &arg[1]);
} else if (strcmp(arg[0], "plugin") == 0) { } else if (strcmp(arg[0], "plugin") == 0) {
MDIPlugin(lmp, narg - 1, &arg[1]); MDIPlugin(lmp, narg - 1, &arg[1]);
} else
error->all(FLERR, "Illegal mdi command"); } else if (strcmp(arg[0], "start") == 0) {
MDI_Comm mdicomm;
MDI_Get_communicator(&mdicomm, 0);
if (mdicomm == MDI_COMM_NULL) {
MDI_Accept_communicator(&mdicomm);
if (mdicomm == MDI_COMM_NULL)
error->all(FLERR, "MDI unable to connect to stand-alone engine");
} else error->all(FLERR, "Cannot use mdi start in plugin mode");
lmp->mdicomm = mdicomm;
} else if (strcmp(arg[0], "stop") == 0) {
MDI_Comm mdicomm = lmp->mdicomm;
int ierr = MDI_Send_command("EXIT", mdicomm);
if (ierr) error->all(FLERR, "MDI: EXIT command");
lmp->mdicomm = MDI_COMM_NULL;
} else error->all(FLERR, "Illegal mdi command");
} }

24
src/lammps.cpp
View File

@ -129,9 +129,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
version = (const char *) LAMMPS_VERSION; version = (const char *) LAMMPS_VERSION;
num_ver = utils::date2num(version); num_ver = utils::date2num(version);
clientserver = 0; external_comm = 0;
cslib = nullptr; mdicomm = 0;
cscomm = 0;
skiprunflag = 0; skiprunflag = 0;
@ -155,19 +154,16 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
#endif #endif
// check if -mpicolor is first arg // check if -mpicolor is first arg
// if so, then 2 apps were launched with one mpirun command // if so, then 2 or more apps were launched with one mpirun command
// this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS // this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS
// e.g. for client/server coupling with another code
// in the future LAMMPS might leverage this in other ways
// universe communicator needs to shrink to be just LAMMPS // universe communicator needs to shrink to be just LAMMPS
// syntax: -mpicolor color // syntax: -mpicolor color
// color = integer for this app, different than other app(s) // color = integer for this app, different than any other app(s)
// do the following: // do the following:
// perform an MPI_Comm_split() to create a new LAMMPS-only subcomm // perform an MPI_Comm_split() to create a new LAMMPS-only subcomm
// NOTE: this assumes other app(s) does same thing, else will hang! // NOTE: this assumes other app(s) make same call, else will hang!
// re-create universe with subcomm // re-create universe with subcomm
// store full multi-app comm in cscomm // store comm that all apps belong to in external_comm
// cscomm is used by CSLIB package to exchange messages w/ other app
int iarg = 1; int iarg = 1;
if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpicolor") == 0 || if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpicolor") == 0 ||
@ -178,7 +174,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
int color = atoi(arg[iarg+1]); int color = atoi(arg[iarg+1]);
MPI_Comm subcomm; MPI_Comm subcomm;
MPI_Comm_split(communicator,color,me,&subcomm); MPI_Comm_split(communicator,color,me,&subcomm);
cscomm = communicator; external_comm = communicator;
communicator = subcomm; communicator = subcomm;
delete universe; delete universe;
universe = new Universe(this,communicator); universe = new Universe(this,communicator);
@ -290,7 +286,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
logflag = iarg + 1; logflag = iarg + 1;
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"-mpi") == 0 || } else if (strcmp(arg[iarg],"-mpicolor") == 0 ||
strcmp(arg[iarg],"-m") == 0) { strcmp(arg[iarg],"-m") == 0) {
if (iarg+2 > narg) if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument"); error->universe_all(FLERR,"Invalid command-line argument");
@ -762,13 +758,13 @@ LAMMPS::~LAMMPS()
delete [] suffix2; delete [] suffix2;
delete [] suffixp; delete [] suffixp;
// free the MPI comm created by -mpi command-line arg processed in constructor // free the MPI comm created by -mpicolor cmdline arg processed in constructor
// it was passed to universe as if original universe world // it was passed to universe as if original universe world
// may have been split later by partitions, universe will free the splits // may have been split later by partitions, universe will free the splits
// free a copy of uorig here, so check in universe destructor will still work // free a copy of uorig here, so check in universe destructor will still work
MPI_Comm copy = universe->uorig; MPI_Comm copy = universe->uorig;
if (cscomm) MPI_Comm_free(&copy); if (external_comm) MPI_Comm_free(&copy);
delete input; delete input;
delete universe; delete universe;

12
src/lammps.h
View File

@ -61,13 +61,15 @@ class LAMMPS {
char *suffix, *suffix2, *suffixp; // suffixes to add to input script style names char *suffix, *suffix2, *suffixp; // suffixes to add to input script style names
int suffix_enable; // 1 if suffixes are enabled, 0 if disabled int suffix_enable; // 1 if suffixes are enabled, 0 if disabled
char *exename; // pointer to argv[0] char *exename; // pointer to argv[0]
//
char ***packargs; // arguments for cmdline package commands char ***packargs; // arguments for cmdline package commands
int num_package; // number of cmdline package commands int num_package; // number of cmdline package commands
//
int clientserver; // 0 = neither, 1 = client, 2 = server MPI_Comm external_comm; // MPI comm encompassing external programs
void *cslib; // client/server messaging via CSlib // when multiple programs launched by mpirun
MPI_Comm cscomm; // MPI comm for client+server in mpi/one mode // set by -mpicolor command line arg
int mdicomm; // for use with MDI code coupling library
const char *match_style(const char *style, const char *name); const char *match_style(const char *style, const char *name);
static const char *installed_packages[]; static const char *installed_packages[];