diff --git a/examples/mdi/README b/examples/mdi/README index 9380e2e79a..9ab3a3baf6 100644 --- a/examples/mdi/README +++ b/examples/mdi/README @@ -36,7 +36,7 @@ using same the same version of MPI. 5 use-case examples are explained below. See the Run.sh file for commands to run each of the examples -in all the different modes. +in all the different modes. Type "sh Run.sh" to run them all. In the first 3 examples, results running with MDI should be identical to running without MDI (alone log files). Example #4 has no non-MDI @@ -130,5 +130,5 @@ used to link to the 2 engines as a plugin libraries. The example run commands below use the default values of the optional switch. The switch is also explained the top of the file; the info is copied here: -# -nsteps 5 -# number of timesteps in dynamics runs, default = 5 +# -nsteps 10 +# number of timesteps in dynamics runs, default = 10 diff --git a/examples/mdi/Run.sh b/examples/mdi/Run.sh index 55c5638841..934b25d4e1 100644 --- a/examples/mdi/Run.sh +++ b/examples/mdi/Run.sh @@ -227,30 +227,30 @@ mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name # Run with TCP: 1 proc each -python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" & +python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.1 & -lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.1 -in in.aimd.mm & +lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.1 -in in.aimdpy.mm & -lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.1 -in in.aimd.qm +lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.1 -in in.aimdpy.qm # --- # Run with TCP: 2 procs + 2 procs + 3 procs -mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" & +mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.2 & -mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm.tcp.2 -in in.aimd.mm & +mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.2 -in in.aimdpy.mm & -mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm.tcp.3 -in in.aimd.qm +mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.3 -in in.aimdpy.qm # --- # Run with MPI: 1 proc each -mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm.mpi.1 -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm.qm.1 -in in.aimd.qm +mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.1 -in in.aimdpy.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.1 -in in.aimdpy.qm > log.aimdpy.driver.mpi.1 # --- # Run with MPI: 2 procs + 2 procs + 3 procs -mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm.mpi.2 -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm.mpi.3 -in in.aimd.qm +mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.2 -in in.aimdpy.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.3 -in in.aimdpy.qm > log.aimdpy.driver.mpi.2 diff --git a/examples/mdi/aimd_driver.py b/examples/mdi/aimd_driver.py index 2d8fe10c1a..cb01a85e42 100644 --- a/examples/mdi/aimd_driver.py +++ b/examples/mdi/aimd_driver.py @@ -23,8 +23,8 @@ # -plugin_args arglist # args to add when launching plugin library, only when using plugin mode # enclose arglist in quotes if multiple words -# -nsteps 5 -# number of timesteps, default = 5 +# -nsteps 10 +# number of timesteps, default = 10 import sys,math,random import mdi @@ -183,7 +183,7 @@ mdiarg = "" plugin = "" plugin_args = "" -nsteps = 5 +nsteps = 10 # parse command-line args diff --git a/examples/mdi/data.series.0.7 b/examples/mdi/data.series.0.7 new file mode 100644 index 0000000000..641d8b07c9 --- /dev/null +++ b/examples/mdi/data.series.0.7 @@ -0,0 +1,1018 @@ +LAMMPS data file via write_data, version 2 Jun 2022, timestep = 0 + +500 atoms +1 atom types + +0 8.939035350965677 xlo xhi +0 8.939035350965677 ylo yhi +0 8.939035350965677 zlo zhi + +Masses + +1 1 + +Atoms # atomic + +1 1 0 0 0 0 0 0 +2 1 0.8939035350965676 0.8939035350965676 0 0 0 0 +3 1 0.8939035350965676 0 0.8939035350965676 0 0 0 +4 1 0 0.8939035350965676 0.8939035350965676 0 0 0 +5 1 1.7878070701931352 0 0 0 0 0 +6 1 2.6817106052897026 0.8939035350965676 0 0 0 0 +7 1 2.6817106052897026 0 0.8939035350965676 0 0 0 +8 1 1.7878070701931352 0.8939035350965676 0.8939035350965676 0 0 0 +9 1 3.5756141403862705 0 0 0 0 0 +10 1 4.469517675482838 0.8939035350965676 0 0 0 0 +11 1 4.469517675482838 0 0.8939035350965676 0 0 0 +12 1 3.5756141403862705 0.8939035350965676 0.8939035350965676 0 0 0 +13 1 5.363421210579405 0 0 0 0 0 +14 1 6.257324745675973 0.8939035350965676 0 0 0 0 +15 1 6.257324745675973 0 0.8939035350965676 0 0 0 +16 1 5.363421210579405 0.8939035350965676 0.8939035350965676 0 0 0 +17 1 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custom step temp pe etotal press vol thermo 1 -run 5 +run 10 diff --git a/examples/mdi/in.aimd.driver b/examples/mdi/in.aimd.driver index b21826d831..652048b6c4 100644 --- a/examples/mdi/in.aimd.driver +++ b/examples/mdi/in.aimd.driver @@ -28,4 +28,4 @@ fix 2 all mdi/qm virial yes thermo_style custom step temp pe etotal press vol thermo 1 -run 5 +run 10 diff --git a/examples/mdi/in.aimd.driver.plugin b/examples/mdi/in.aimd.driver.plugin index 97514cbcd2..a021f12b07 100644 --- a/examples/mdi/in.aimd.driver.plugin +++ b/examples/mdi/in.aimd.driver.plugin @@ -30,4 +30,4 @@ thermo 1 mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" & infile in.aimd.engine extra "-log log.aimd.engine.plugin" & - command "run 5" + command "run 10" diff --git a/examples/mdi/in.aimd.engine b/examples/mdi/in.aimd.engine index f3293e048d..a64d166a24 100644 --- a/examples/mdi/in.aimd.engine +++ b/examples/mdi/in.aimd.engine @@ -14,4 +14,7 @@ pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes +thermo_style custom step temp pe etotal press vol +thermo 1 + mdi engine diff --git a/examples/mdi/in.aimd.mm b/examples/mdi/in.aimdpy.mm similarity index 100% rename from examples/mdi/in.aimd.mm rename to examples/mdi/in.aimdpy.mm diff --git a/examples/mdi/in.aimd.qm b/examples/mdi/in.aimdpy.qm similarity index 100% rename from examples/mdi/in.aimd.qm rename to examples/mdi/in.aimdpy.qm diff --git a/examples/mdi/in.series.alone b/examples/mdi/in.series.alone index f359581c50..2e17468507 100644 --- a/examples/mdi/in.series.alone +++ b/examples/mdi/in.series.alone @@ -11,11 +11,7 @@ label LOOP units lj atom_style atomic - lattice fcc ${rho} - region box block 0 $x 0 $y 0 $z - create_box 1 box - create_atoms 1 box - mass 1 1.0 + read_data data.series.${rho} displace_atoms all random 0.1 0.1 0.1 48294 diff --git a/examples/mdi/in.series.driver b/examples/mdi/in.series.driver index 4089dd66ec..267df465fc 100644 --- a/examples/mdi/in.series.driver +++ b/examples/mdi/in.series.driver @@ -13,11 +13,7 @@ label LOOP units lj atom_style atomic - lattice fcc ${rho} - region box block 0 $x 0 $y 0 $z - create_box 1 box - create_atoms 1 box - mass 1 1.0 + read_data data.series.${rho} displace_atoms all random 0.1 0.1 0.1 48294 @@ -25,9 +21,9 @@ label LOOP neigh_modify delay 0 every 1 check yes fix 1 all mdi/qm add no virial yes connect no - variable epress equal (f_1[1]+f_1[2]+f_1[3])/3 + variable evirial 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] + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] run 0 diff --git a/examples/mdi/in.series.driver.plugin b/examples/mdi/in.series.driver.plugin index 8096b56886..f1189940b4 100644 --- a/examples/mdi/in.series.driver.plugin +++ b/examples/mdi/in.series.driver.plugin @@ -11,11 +11,7 @@ label LOOP units lj atom_style atomic - lattice fcc ${rho} - region box block 0 $x 0 $y 0 $z - create_box 1 box - create_atoms 1 box - mass 1 1.0 + read_data data.series.${rho} displace_atoms all random 0.1 0.1 0.1 48294 @@ -23,9 +19,9 @@ label LOOP 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 + variable evirial 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] + thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3] mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" & infile in.series.engine & diff --git a/examples/mdi/in.snapshot.alone b/examples/mdi/in.snapshot.alone index cf9683be3f..7633dcaae3 100644 --- a/examples/mdi/in.snapshot.alone +++ b/examples/mdi/in.snapshot.alone @@ -1,17 +1,9 @@ # 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 +read_data data.snapshot velocity all create 1.44 87287 loop geom @@ -29,8 +21,8 @@ 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 & +dump 1 all custom 100 dump.snapshot.alone & id type x y z fx fy fz dump_modify 1 sort id -run 1500 +run 300 diff --git a/examples/mdi/in.snapshot.driver b/examples/mdi/in.snapshot.driver index 607a52a456..78205efb0f 100644 --- a/examples/mdi/in.snapshot.driver +++ b/examples/mdi/in.snapshot.driver @@ -1,17 +1,9 @@ # 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 +read_data data.snapshot velocity all create 1.44 87287 loop geom @@ -23,19 +15,19 @@ neigh_modify delay 0 every 1 check yes fix 1 all nve -fix 2 all mdi/qm add no every 500 virial yes +fix 2 all mdi/qm add no every 100 virial yes compute 1 all pressure NULL virial -variable epress equal (f_2[1]+f_2[2]+f_2[3])/3 +variable evirial 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 & +dump 1 all custom 100 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 & +run 300 pre no post no every 100 & "print 'QM eng = $(f_2/atoms)'" & - "print 'QM virial = $(v_epress) $(f_2[1]) $(f_2[2]) $(f_2[3])'" + "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" diff --git a/examples/mdi/in.snapshot.driver.plugin b/examples/mdi/in.snapshot.driver.plugin index 2fdca3f6cd..37f0fba2f9 100644 --- a/examples/mdi/in.snapshot.driver.plugin +++ b/examples/mdi/in.snapshot.driver.plugin @@ -7,11 +7,7 @@ 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 +read_data data.snapshot velocity all create 1.44 87287 loop geom @@ -23,16 +19,16 @@ neigh_modify delay 0 every 1 check yes fix 1 all nve -fix 2 all mdi/qm add no every 500 virial yes +fix 2 all mdi/qm add no every 100 virial yes compute 1 all pressure NULL virial -variable epress equal (f_2[1]+f_2[2]+f_2[3])/3 +variable evirial 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.plugin & +dump 1 all custom 100 dump.snapshot.driver.plugin & id type x y z f_2[1] f_2[2] f_2[3] dump_modify 1 sort id @@ -40,7 +36,7 @@ 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 + run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" - "print 'QM virial = $(v_epress) $(f_2[1]) $(f_2[2]) $(f_2[3])'" + "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'" """ diff --git a/src/MDI/fix_mdi_qm.cpp b/src/MDI/fix_mdi_qm.cpp index 99f23f7e59..0b05263f01 100644 --- a/src/MDI/fix_mdi_qm.cpp +++ b/src/MDI/fix_mdi_qm.cpp @@ -344,11 +344,19 @@ void FixMDIQM::post_force(int vflag) } // optionally set fix->virial - // divide by nprocs so each proc stores a portion + // multiply by volume to make it extensive + // divide by nprocs so each proc stores a portion + // this is b/c ComputePressure expects that as input from a fix + // it will do an MPI_Allreduce and divide by volume if (virialflag && addflag) { + double volume; + if (domain->dimension == 2) + volume = domain->xprd * domain->yprd; + else if (domain->dimension == 3) + volume = domain->xprd * domain->yprd * domain->zprd; for (int i = 0; i < 6; i++) - virial[i] = qm_virial[i]/nprocs; + virial[i] = qm_virial[i]*volume/nprocs; } }