diff --git a/examples/QM/LATTE/2uo2.lmp b/examples/QM/LATTE/2uo2.lmp new file mode 100644 index 0000000000..e879f20a19 --- /dev/null +++ b/examples/QM/LATTE/2uo2.lmp @@ -0,0 +1,24 @@ + LAMMPS Description + + 6 atoms + + 2 atom types + + 0.0000000000000000 10.800000000000001 xlo xhi + 0.0000000000000000 5.4000000000000004 ylo yhi + 0.0000000000000000 5.4000000000000004 zlo zhi + 3.3065463576978537E-016 3.3065463576978537E-016 3.3065463576978537E-016 xy xz yz + + Masses + + 1 238.05078125000000 + 2 15.994915008544922 + + Atoms + + 1 1 1 0.0 2.70000 8.10000 0.00000 + 2 1 2 0.0 1.35000 9.45000 1.35000 + 3 1 2 0.0 4.05000 9.45000 1.35000 + 4 1 1 0.0 2.70000 10.80000 2.70000 + 5 1 2 0.0 1.35000 12.15000 4.05000 + 6 1 2 0.0 4.05000 12.15000 4.05000 diff --git a/examples/QM/LATTE/3uo2.lmp b/examples/QM/LATTE/3uo2.lmp new file mode 100644 index 0000000000..bbbab023fc --- /dev/null +++ b/examples/QM/LATTE/3uo2.lmp @@ -0,0 +1,27 @@ + LAMMPS Description + + 9 atoms + + 2 atom types + + 0.0000000000000000 16.199999999999999 xlo xhi + 0.0000000000000000 5.4000000000000004 ylo yhi + 0.0000000000000000 5.4000000000000004 zlo zhi + 3.3065463576978537E-016 3.3065463576978537E-016 3.3065463576978537E-016 xy xz yz + + Masses + + 1 238.05078125000000 + 2 15.994915008544922 + + Atoms + + 1 1 1 0.0 2.70000 8.10000 0.00000 + 2 1 2 0.0 1.35000 9.45000 1.35000 + 3 1 2 0.0 4.05000 9.45000 1.35000 + 4 1 1 0.0 2.70000 10.80000 2.70000 + 5 1 2 0.0 1.35000 12.15000 4.05000 + 6 1 2 0.0 4.05000 12.15000 4.05000 + 7 1 1 0.0 2.70000 13.50000 5.40000 + 8 1 2 0.0 1.35000 14.85000 6.75000 + 9 1 2 0.0 4.05000 14.85000 6.75000 diff --git a/examples/QM/LATTE/4uo2.lmp b/examples/QM/LATTE/4uo2.lmp new file mode 100644 index 0000000000..67cd351d9d --- /dev/null +++ b/examples/QM/LATTE/4uo2.lmp @@ -0,0 +1,30 @@ + LAMMPS Description + + 12 atoms + + 2 atom types + + 0.0000000000000000 10.800000000000001 xlo xhi + 0.0000000000000000 10.800000000000001 ylo yhi + 0.0000000000000000 5.4000000000000004 zlo zhi + 6.6130927153957075E-016 3.3065463576978537E-016 3.3065463576978537E-016 xy xz yz + + Masses + + 1 238.05078125000000 + 2 15.994915008544922 + + Atoms + + 1 1 1 0.0 2.70000 8.10000 0.00000 + 2 1 2 0.0 1.35000 9.45000 1.35000 + 3 1 2 0.0 4.05000 9.45000 1.35000 + 4 1 1 0.0 5.40000 8.10000 2.70000 + 5 1 2 0.0 4.05000 9.45000 4.05000 + 6 1 2 0.0 6.75000 9.45000 4.05000 + 7 1 1 0.0 2.70000 10.80000 2.70000 + 8 1 2 0.0 1.35000 12.15000 4.05000 + 9 1 2 0.0 4.05000 12.15000 4.05000 + 10 1 1 0.0 5.40000 10.80000 5.40000 + 11 1 2 0.0 4.05000 12.15000 6.75000 + 12 1 2 0.0 6.75000 12.15000 6.75000 diff --git a/examples/QM/LATTE/README b/examples/QM/LATTE/README new file mode 100644 index 0000000000..81fd6d614a --- /dev/null +++ b/examples/QM/LATTE/README @@ -0,0 +1,130 @@ +LATTE is a semi-empirical tight-binding quantum code, developed +primarily at Los Alamos National Labs. + +See these links: + + https://www.osti.gov/biblio/1526907-los-alamos-transferable-tight-binding-energetics-latte-version + https://github.com/lanl/LATTE + +LAMMPS has 2 ways of working with LATTE: + +(1) Via its LATTE package and the fix latte command + must run LAMMPS on a single processor, it calls LATTE as a library + +(2) Via its MDI package and the code-coupling MDI library + (a) can run LAMMPS and LATTE as stand-alone codes + LAMMPS can be run on any number of procs + LATTE must run on a single proc, but can use OpenMP + (b) can run LAMMPS with LATTE as a plug-in library + must run LAMMPS on a single processor + +Examples for use case (1) are in the examples/latte dir. Use case (2) +is illustrated in this dir. + +NOTE: If you compare MDI runs in this dir to similar fix latte runs in +examples/latte, the answers for energy and virial will be differnt. +This is b/c the version of LATTE used by the fix latte command within +the LATTE package is older than the version of LATTE used here which +now has MDI support. + +------------------ +Building 3 codes needed to run these examples + +(1) Download and build MDI + +% git clone git@github.com:MolSSI-MDI/MDI_Library.git mdi +% cd mdi +% mkdir build; cd build +% cmake .. # includes support for all langauges (incl Fortran, Python) +% make + +(2) Download and build LATTE with MDI support + +% git clone git@github.com:lanl/LATTE.git latte +% cd latte +% cp makefiles/makefile.CHOICES.mdi makefile.CHOICES # so can now edit +% edit makefile.CHOICES settings to have these settings: + MAKELIB = OFF, SHARED = ON, MDI = ON + MDI_PATH must point to CMake build of MDI in (1), + e.g. /home/sjplimp/mdi/build/MDI_Library +% make clean +% make # creates liblatte.so and LATTE_DOUBLE with support for MDI + +(3) Build LAMMPS with its MDI package + also with the MOLECULE package for these example scripts + +% cd lammps +% mkdir build; cd build +% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake +% make + +(4) Copy LAMMPS and LATTE files into this dir + +Copy the LAMMPS executable (e.g. lmp_mpi) into this dir. +Copy the LATTE executabe (LATTE_DOUBLE) into this dir. +The run commands below assume you have done this. + +------------------ +Notes on LATTE usage + +By default LATTE reads the latte.in file for its parameters. That +file specifies other files LATTE will read. With MDI, the driver code +(e.g. LAMMPS) can use the >FNAME command to specify an alternate +filename to use instead of latte.in. + +By default LATTE writes out a log.latte file with info about its +calculations. An "OUTFILE= logfile" setting in latte.in can rename +this file. + +This version of LATTE can only run on a single processor in an MPI +context. However LATTE can use OpenMP for parallelism, so that it +effectively runs on more cores. See instructions below for how to do +this. + +--------- +Run example #1: AIMD + +* Run with MPI: 1 proc each + +mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \ + -in in.aimd.mdi -log log.aimd.mdi.lammps.1 : \ + -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI" + +* Run with MPI: 2 procs for LAMMPS, 1 for LATTE + +mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \ + -in in.aimd.mdi -log log.aimd.mdi.lammps.2 : \ + -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI" + +* Run in plugin mode: 1 proc + +lmp_mpi -mdi \ + "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \ + -in in.aimd.mdi.plugin -log log.aimd.mdi.plugin.lammps.1 + +NOTE: The -plugin_path setting needs to point to where you built LATTE +in step (2). + +--------- +Run example #2: sequence of configurations + +* Run with MPI: 1 proc each + +mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \ + -in in.series.mdi -log log.series.mdi.lammps.1 : \ + -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI" + +* Run with MPI: 2 procs for LAMMPS, 1 for LATTE + +mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \ + -in in.series.mdi -log log.series.mdi.lammps.2 : \ + -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI" + +* Run in plugin mode: 1 proc + +lmp_mpi -mdi \ + "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \ + -in in.series.mdi.plugin -log log.series.mdi.plugin.1 + +NOTE: The -plugin_path setting needs to point to where you built LATTE +in step (2). diff --git a/examples/QM/LATTE/bondints.table b/examples/QM/LATTE/bondints.table new file mode 100644 index 0000000000..568da2e1c2 --- /dev/null +++ b/examples/QM/LATTE/bondints.table @@ -0,0 +1,1384 @@ + Noint= 31 + U U sss + 41 + 0.200000 0.973630 -13.481772 + 0.400000 0.905246 -9.285695 + 0.600000 0.815561 -5.700568 + 0.800000 0.720128 -3.638461 + 1.000000 0.626372 -2.259606 + 1.200000 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0.023293 + 4.700000 -0.000883 0.017442 + 4.800000 -0.000567 0.012300 + 4.900000 -0.000312 0.007973 diff --git a/examples/QM/LATTE/electrons.dat b/examples/QM/LATTE/electrons.dat new file mode 100644 index 0000000000..a7ef400ed6 --- /dev/null +++ b/examples/QM/LATTE/electrons.dat @@ -0,0 +1,15 @@ +Noelem= 2 +Element basis Numel Es Ep Ed Ef Mass HubbardU Wss Wpp Wdd Wff +U sdf 6.0 -4.08 0.0 0.816 -0.586 238.05078 9.0 0.0 0.0 0.0 0.0 +O sp 6.0 -23.77 -8.85 0.0 0.0 15.994915 12.2 0.0 0.0 0.0 0.0 + + +W spd 6.0 -4.52 0.53 -2.91 0.0 183.84 7.048 0.0 0.0 0.0 0.0 +Mo sd 6.0 -3.29 0.0 -1.98 0.0 95.95 6.48 0.0 0.0 0.0 0.0 +S sp 6.0 -14.00 -3.97 0.0 0.0 32.06 8.28 0.0 -0.4278 0.0 0.0 + + +N sp 5.000000 -18.543798 -7.862407 0.000000 0.000000 14.006700 17.053958 0.000000 -0.6934 0.000000 0.000000 +H s 1.000000 -6.237968 0.000000 0.000000 0.000000 1.007900 13.684855 -2.23400 0.000000 0.000000 0.000000 +C sp 4.000000 -13.736556 -4.748938 0.000000 0.000000 12.010000 10.522540 0.000000 -0.618100 0.000000 0.000000 +O sp 6.000000 -23.833752 -9.645001 0.000000 0.000000 15.999400 14.443874 0.000000 -0.757650 0.000000 0.000000 diff --git a/examples/QM/LATTE/in.aimd.fixlatte b/examples/QM/LATTE/in.aimd.fixlatte new file mode 100644 index 0000000000..83e77270e2 --- /dev/null +++ b/examples/QM/LATTE/in.aimd.fixlatte @@ -0,0 +1,27 @@ +# AIMD test of two UO2 molecules with LATTE with fix latte + +units metal +atom_style full +atom_modify sort 0 0.0 + +read_data 2uo2.lmp + +velocity all create 300.0 87287 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press +thermo 1 + +dump 1 all custom 1 dump.aimd & + id type x y z vx vy vz fx fy fz + +run 20 diff --git a/examples/QM/LATTE/in.aimd.mdi b/examples/QM/LATTE/in.aimd.mdi new file mode 100644 index 0000000000..f158065997 --- /dev/null +++ b/examples/QM/LATTE/in.aimd.mdi @@ -0,0 +1,26 @@ +# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode + +units metal +atom_style full +atom_modify sort 0 0.0 + +read_data 2uo2.lmp + +velocity all create 300.0 87287 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all mdi/qm virial yes elements 92 8 + +thermo_style custom step temp pe etotal press +thermo 1 + +dump 1 all custom 1 dump.aimd.mdi & + id type x y z vx vy vz fx fy fz + +run 20 diff --git a/examples/QM/LATTE/in.aimd.mdi.plugin b/examples/QM/LATTE/in.aimd.mdi.plugin new file mode 100644 index 0000000000..93f9374f42 --- /dev/null +++ b/examples/QM/LATTE/in.aimd.mdi.plugin @@ -0,0 +1,27 @@ +# AIMD test of two UO2 molecules with LATTE in MDI plugin mode + +units metal +atom_style full +atom_modify sort 0 0.0 + +read_data 2uo2.lmp + +velocity all create 300.0 87287 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all mdi/qm virial yes elements 92 8 + +thermo_style custom step temp pe etotal press +thermo 1 + +dump 1 all custom 1 dump.aimd.mdi.plugin & + id type x y z vx vy vz fx fy fz + +mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" & + command "run 20" diff --git a/examples/QM/LATTE/in.series.mdi b/examples/QM/LATTE/in.series.mdi new file mode 100644 index 0000000000..60943e03d8 --- /dev/null +++ b/examples/QM/LATTE/in.series.mdi @@ -0,0 +1,37 @@ +# Series of single-point calcs of 2,3,4 UO2 molecules +# with LATTE in MDI stand-alone mode + +variable files index 2uo2 3uo2 4uo2 + +mdi connect + +label LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + timestep 0.001 + + fix 1 all mdi/qm virial yes elements 92 8 connect no + + thermo_style custom step temp pe etotal press + thermo 1 + + run 0 + + write_dump all custom dump.series.${files} & + id type x y z fx fy fz modify sort id + + clear + +next files + +jump SELF LOOP + +mdi exit diff --git a/examples/QM/LATTE/in.series.mdi.plugin b/examples/QM/LATTE/in.series.mdi.plugin new file mode 100644 index 0000000000..0985503746 --- /dev/null +++ b/examples/QM/LATTE/in.series.mdi.plugin @@ -0,0 +1,32 @@ +# Series of single-point calcs of 2,3,4 UO2 molecules +# with LATTE in MDI plugin mode + +variable files index 2uo2 3uo2 4uo2 + +label LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + fix 1 all mdi/qm virial yes elements 92 8 + + thermo_style custom step temp pe etotal press + thermo 1 + + mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" & + command "run 0" + + write_dump all custom dump.series.plugin.${files} & + id type x y z fx fy fz modify sort id + + clear + +next files + +jump SELF LOOP diff --git a/examples/QM/LATTE/latte.in b/examples/QM/LATTE/latte.in new file mode 100755 index 0000000000..5786bb6588 --- /dev/null +++ b/examples/QM/LATTE/latte.in @@ -0,0 +1,67 @@ +#General controls +CONTROL{ + XCONTROL= 1 + BASISTYPE= NONORTHO + PARAMPATH= './' + SCLTYPE= TABLE + DEBUGON= 0 + FERMIM= 6 + CGORLIB= 1 CGTOL= 1.0e-6 + KBT= 1.0 + NORECS= 5 + ENTROPYKIND= 1 + PPOTON= 2 VDWON= 0 + SPINON= 0 SPINTOL= 1.0e-4 + ELECTRO= 1 ELECMETH= 0 ELEC_ETOL= 0.001 ELEC_QTOL= 1.0e-12 + COULACC= 1.0e-6 COULCUT= -500.0 COULR1= 500.0 + MAXSCF= 250 + BREAKTOL= 1.0E-12 MINSP2ITER= 22 SP2CONV= REL + FULLQCONV= 1 QITER= 0 + QMIX= 0.05 SPINMIX= 0.05 MDMIX= 0.05 + #QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25 + ORDERNMOL= 0 + SPARSEON= 0 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4 + MSPARSE= 3000 + LCNON= 0 LCNITER= 4 CHTOL= 0.01 + SKIN= 1.0 + RELAX= 0 RELAXTYPE= SD MAXITER= 100 RLXFTOL= 0.001 + MDON= 1 + PBCON= 1 + RESTART= 0 + CHARGE= 0 + XBO= 1 + XBODISON= 1 + XBODISORDER= 5 + NGPU= 2 + KON= 0 + COMPFORCE= 1 + DOSFIT= 0 INTS2FIT= 1 BETA= 1000.0 NFITSTEP= 5000 QFIT= 0 MCSIGMA= 0.2 + PPFITON= 0 + ALLFITON= 0 + PPSTEP= 500 BISTEP= 500 PP2FIT= 2 BINT2FIT= 6 + PPBETA= 1000.0 PPSIGMA= 0.01 PPNMOL= 10 PPNGEOM= 200 + PARREP= 0 + ER= 1.0 + #DOKERNEL= T +} + +MDCONTROL{ +MAXITER= 2000 +UDNEIGH= 1 +DT= 0.5 +TEMPERATURE= 1.0e-10 RNDIST= GAUSSIAN SEEDINIT= UNIFORM +DUMPFREQ= 250 +RSFREQ= 500 +WRTFREQ= 1 +TOINITTEMP5= 1 +THERMPER= 500 +THERMRUN= 50000 +NVTON= 0 NPTON= 0 AVEPER= 1000 FRICTION= 1000.0 SEED= 54 +PTARGET= 0.0 NPTTYPE= ISO +SHOCKON= 0 +SHOCKSTART= 100000 +SHOCKDIR= 1 +UPARTICLE= 500.0 USHOCK= -4590.0 C0= 1300.0 +MDADAPT= 0 +GETHUG= 0 E0= -795.725 V0= 896.984864 P0= 0.083149 +} diff --git a/examples/QM/LATTE/log.aimd.mdi.lammps.1 b/examples/QM/LATTE/log.aimd.mdi.lammps.1 new file mode 100644 index 0000000000..a9cda0b8b4 --- /dev/null +++ b/examples/QM/LATTE/log.aimd.mdi.lammps.1 @@ -0,0 +1,100 @@ +LAMMPS (23 Jun 2022) +# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode + +units metal +atom_style full +atom_modify sort 0 0.0 + +read_data 2uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 6 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +velocity all create 300.0 87287 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all mdi/qm virial yes elements 92 8 + +thermo_style custom step temp pe etotal press +thermo 1 + +dump 1 all custom 1 dump.aimd.mdi id type x y z vx vy vz fx fy fz + +run 20 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 10.8, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes + Step Temp PotEng TotEng Press + 0 300 -50.539035 -50.345145 -120197.6 + 1 307.57345 -50.544722 -50.345937 -120123.27 + 2 316.3757 -50.551342 -50.346868 -120035.12 + 3 326.39203 -50.558885 -50.347938 -119933.11 + 4 337.60559 -50.567341 -50.349146 -119817.17 + 5 349.99734 -50.576697 -50.350493 -119687.24 + 6 363.54606 -50.586939 -50.351979 -119543.23 + 7 378.22834 -50.598054 -50.353605 -119385.07 + 8 394.0186 -50.610024 -50.355369 -119212.67 + 9 410.88903 -50.622831 -50.357273 -119025.94 + 10 428.80963 -50.636457 -50.359317 -118824.77 + 11 447.74819 -50.65088 -50.3615 -118609.06 + 12 467.67027 -50.666079 -50.363823 -118378.7 + 13 488.53922 -50.68203 -50.366287 -118133.58 + 14 510.31617 -50.698708 -50.36889 -117873.58 + 15 532.96002 -50.716086 -50.371633 -117598.57 + 16 556.42747 -50.734137 -50.374517 -117308.44 + 17 580.67298 -50.75283 -50.377541 -117003.05 + 18 605.64879 -50.772136 -50.380705 -116682.27 + 19 631.30497 -50.792023 -50.38401 -116345.95 + 20 657.58937 -50.812455 -50.387454 -115993.97 +Loop time of 3.33709 on 1 procs for 20 steps with 6 atoms + +Performance: 0.129 ns/day, 185.394 hours/ns, 5.993 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 8.02e-07 | 8.02e-07 | 8.02e-07 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 4.5469e-05 | 4.5469e-05 | 4.5469e-05 | 0.0 | 0.00 +Output | 0.00079115 | 0.00079115 | 0.00079115 | 0.0 | 0.02 +Modify | 3.3362 | 3.3362 | 3.3362 | 0.0 | 99.97 +Other | | 1.728e-05 | | | 0.00 + +Nlocal: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/QM/LATTE/log.aimd.mdi.lammps.2 b/examples/QM/LATTE/log.aimd.mdi.lammps.2 new file mode 100644 index 0000000000..476a000d51 --- /dev/null +++ b/examples/QM/LATTE/log.aimd.mdi.lammps.2 @@ -0,0 +1,102 @@ +LAMMPS (23 Jun 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode + +units metal +atom_style full +atom_modify sort 0 0.0 + +read_data 2uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16) + 2 by 1 by 1 MPI processor grid + reading atoms ... + 6 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +velocity all create 300.0 87287 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all mdi/qm virial yes elements 92 8 + +thermo_style custom step temp pe etotal press +thermo 1 + +dump 1 all custom 1 dump.aimd.mdi id type x y z vx vy vz fx fy fz + +run 20 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 10.8, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 5.485 | 5.987 | 6.489 Mbytes + Step Temp PotEng TotEng Press + 0 300 -50.539035 -50.345145 -120197.6 + 1 307.57345 -50.544722 -50.345937 -120123.27 + 2 316.3757 -50.551342 -50.346868 -120035.12 + 3 326.39203 -50.558885 -50.347938 -119933.11 + 4 337.60559 -50.567341 -50.349146 -119817.17 + 5 349.99734 -50.576697 -50.350493 -119687.24 + 6 363.54606 -50.586939 -50.351979 -119543.23 + 7 378.22834 -50.598054 -50.353605 -119385.07 + 8 394.0186 -50.610024 -50.355369 -119212.67 + 9 410.88903 -50.622831 -50.357273 -119025.94 + 10 428.80963 -50.636457 -50.359317 -118824.77 + 11 447.74819 -50.65088 -50.3615 -118609.06 + 12 467.67027 -50.666079 -50.363823 -118378.7 + 13 488.53922 -50.68203 -50.366287 -118133.58 + 14 510.31617 -50.698708 -50.36889 -117873.58 + 15 532.96002 -50.716086 -50.371633 -117598.57 + 16 556.42747 -50.734137 -50.374517 -117308.44 + 17 580.67298 -50.75283 -50.377541 -117003.05 + 18 605.64879 -50.772136 -50.380705 -116682.27 + 19 631.30497 -50.792023 -50.38401 -116345.95 + 20 657.58937 -50.812455 -50.387454 -115993.97 +Loop time of 25.1385 on 2 procs for 20 steps with 6 atoms + +Performance: 0.017 ns/day, 1396.581 hours/ns, 0.796 timesteps/s +99.9% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 9.94e-07 | 1.4045e-06 | 1.815e-06 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.6802e-05 | 2.4755e-05 | 3.2708e-05 | 0.0 | 0.00 +Output | 0.001682 | 0.0018221 | 0.0019621 | 0.3 | 0.01 +Modify | 25.136 | 25.136 | 25.136 | 0.0 | 99.99 +Other | | 0.0002258 | | | 0.00 + +Nlocal: 3 ave 6 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 1 ave 2 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:26 diff --git a/examples/QM/LATTE/log.aimd.mdi.plugin.lammps.1 b/examples/QM/LATTE/log.aimd.mdi.plugin.lammps.1 new file mode 100644 index 0000000000..e2c39a69af --- /dev/null +++ b/examples/QM/LATTE/log.aimd.mdi.plugin.lammps.1 @@ -0,0 +1,100 @@ +LAMMPS (23 Jun 2022) +# AIMD test of two UO2 molecules with LATTE in MDI plugin mode + +units metal +atom_style full +atom_modify sort 0 0.0 + +read_data 2uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 6 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +velocity all create 300.0 87287 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all mdi/qm virial yes elements 92 8 + +thermo_style custom step temp pe etotal press +thermo 1 + +dump 1 all custom 1 dump.aimd.mdi.plugin id type x y z vx vy vz fx fy fz + +mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 20" +run 20 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 10.8, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes + Step Temp PotEng TotEng Press + 0 300 -50.539035 -50.345145 -120197.6 + 1 307.57345 -50.544722 -50.345937 -120123.27 + 2 316.3757 -50.551342 -50.346868 -120035.12 + 3 326.39203 -50.558885 -50.347938 -119933.11 + 4 337.60559 -50.567341 -50.349146 -119817.17 + 5 349.99734 -50.576697 -50.350493 -119687.24 + 6 363.54606 -50.586939 -50.351979 -119543.23 + 7 378.22834 -50.598054 -50.353605 -119385.07 + 8 394.0186 -50.610024 -50.355369 -119212.67 + 9 410.88903 -50.622831 -50.357273 -119025.94 + 10 428.80963 -50.636457 -50.359317 -118824.77 + 11 447.74819 -50.65088 -50.3615 -118609.06 + 12 467.67027 -50.666079 -50.363823 -118378.7 + 13 488.53922 -50.68203 -50.366287 -118133.58 + 14 510.31617 -50.698708 -50.36889 -117873.58 + 15 532.96002 -50.716086 -50.371633 -117598.57 + 16 556.42747 -50.734137 -50.374517 -117308.44 + 17 580.67298 -50.75283 -50.377541 -117003.05 + 18 605.64879 -50.772136 -50.380705 -116682.27 + 19 631.30497 -50.792023 -50.38401 -116345.95 + 20 657.58937 -50.812455 -50.387454 -115993.97 +Loop time of 3.95092 on 1 procs for 20 steps with 6 atoms + +Performance: 0.109 ns/day, 219.496 hours/ns, 5.062 timesteps/s +6752.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 2.132e-06 | 2.132e-06 | 2.132e-06 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 2.3959e-05 | 2.3959e-05 | 2.3959e-05 | 0.0 | 0.00 +Output | 0.0016711 | 0.0016711 | 0.0016711 | 0.0 | 0.04 +Modify | 3.9491 | 3.9491 | 3.9491 | 0.0 | 99.95 +Other | | 8.929e-05 | | | 0.00 + +Nlocal: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/QM/LATTE/log.series.mdi.lammps.1 b/examples/QM/LATTE/log.series.mdi.lammps.1 new file mode 100644 index 0000000000..35db315e74 --- /dev/null +++ b/examples/QM/LATTE/log.series.mdi.lammps.1 @@ -0,0 +1,255 @@ +LAMMPS (23 Jun 2022) +# Series of single-point calcs of 2,3,4 UO2 molecules +# with LATTE in MDI stand-alone mode + +variable files index 2uo2 3uo2 4uo2 + +mdi connect + +label LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + read_data 2uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 6 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + timestep 0.001 + + fix 1 all mdi/qm virial yes elements 92 8 connect no + + thermo_style custom step temp pe etotal press + thermo 1 + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 10.8, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes + Step Temp PotEng TotEng Press + 0 0 -50.539035 -50.539035 -120855.2 +Loop time of 1.107e-06 on 1 procs for 0 steps with 6 atoms + +180.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.107e-06 | | |100.00 + +Nlocal: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id + write_dump all custom dump.series.2uo2 id type x y z fx fy fz modify sort id + + clear + +next files + +jump SELF LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + read_data 3uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 9 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.002 seconds + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + timestep 0.001 + + fix 1 all mdi/qm virial yes elements 92 8 connect no + + thermo_style custom step temp pe etotal press + thermo 1 + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 16.2, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes + Step Temp PotEng TotEng Press + 0 0 -78.155679 -78.155679 -99931.431 +Loop time of 7.43e-07 on 1 procs for 0 steps with 9 atoms + +134.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.43e-07 | | |100.00 + +Nlocal: 9 ave 9 max 9 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id + write_dump all custom dump.series.3uo2 id type x y z fx fy fz modify sort id + + clear + +next files + +jump SELF LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + read_data 4uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 12 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + timestep 0.001 + + fix 1 all mdi/qm virial yes elements 92 8 connect no + + thermo_style custom step temp pe etotal press + thermo 1 + + run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 10.8, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes + Step Temp PotEng TotEng Press + 0 0 -108.3939 -108.3939 -20025.507 +Loop time of 7.65e-07 on 1 procs for 0 steps with 12 atoms + +130.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.65e-07 | | |100.00 + +Nlocal: 12 ave 12 max 12 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5 ave 5 max 5 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id + write_dump all custom dump.series.4uo2 id type x y z fx fy fz modify sort id + + clear + +next files + +jump SELF LOOP + +mdi exit +Total wall time: 0:00:02 diff --git a/examples/QM/LATTE/log.series.mdi.lammps.2 b/examples/QM/LATTE/log.series.mdi.lammps.2 new file mode 100644 index 0000000000..6c57bd22d8 --- /dev/null +++ b/examples/QM/LATTE/log.series.mdi.lammps.2 @@ -0,0 +1,166 @@ +LAMMPS (23 Jun 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Series of single-point calcs of 2,3,4 UO2 molecules +# with LATTE in MDI stand-alone mode + +variable files index 2uo2 3uo2 4uo2 + +mdi connect + +label LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + read_data 2uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16) + 2 by 1 by 1 MPI processor grid + reading atoms ... + 6 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + timestep 0.001 + + fix 1 all mdi/qm virial yes elements 92 8 connect no + + thermo_style custom step temp pe etotal press + thermo 1 + + run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 10.8, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes + Step Temp PotEng TotEng Press + 0 0 -50.539035 -50.539035 -120855.2 +Loop time of 1.987e-06 on 2 procs for 0 steps with 6 atoms + +100.7% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.987e-06 | | |100.00 + +Nlocal: 3 ave 6 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 1 ave 2 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id + write_dump all custom dump.series.2uo2 id type x y z fx fy fz modify sort id + + clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task + +next files + +jump SELF LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + read_data 3uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16) + 2 by 1 by 1 MPI processor grid + reading atoms ... + 9 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + timestep 0.001 + + fix 1 all mdi/qm virial yes elements 92 8 connect no + + thermo_style custom step temp pe etotal press + thermo 1 + + run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 16.2, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes + Step Temp PotEng TotEng Press + 0 0 -78.155679 -78.155679 -99931.431 +Loop time of 1.9115e-06 on 2 procs for 0 steps with 9 atoms + +130.8% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.912e-06 | | |100.00 + +Nlocal: 4.5 ave 9 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 1.5 ave 3 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/QM/LATTE/log.series.mdi.plugin.1 b/examples/QM/LATTE/log.series.mdi.plugin.1 new file mode 100644 index 0000000000..f362e82a6e --- /dev/null +++ b/examples/QM/LATTE/log.series.mdi.plugin.1 @@ -0,0 +1,78 @@ +LAMMPS (23 Jun 2022) +# Series of single-point calcs of 2,3,4 UO2 molecules +# with LATTE in MDI plugin mode + +variable files index 2uo2 3uo2 4uo2 + +label LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + read_data 2uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 6 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + fix 1 all mdi/qm virial yes elements 92 8 + + thermo_style custom step temp pe etotal press + thermo 1 + + mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0" +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 10.8, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes + Step Temp PotEng TotEng Press + 0 0 -50.539035 -50.539035 -120855.2 +Loop time of 1.9634e-05 on 1 procs for 0 steps with 6 atoms + +11301.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.963e-05 | | |100.00 + +Nlocal: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 diff --git a/examples/QM/LATTE/ppots.dftb b/examples/QM/LATTE/ppots.dftb new file mode 100644 index 0000000000..59ba0a04c7 --- /dev/null +++ b/examples/QM/LATTE/ppots.dftb @@ -0,0 +1,178 @@ +3 +U O +101 + 1.0000000000000000 53.452052832272599 + 1.0520000000000000 48.423668742582244 + 1.1040000000000001 43.721445018814535 + 1.1560000000000001 39.334296276283553 + 1.2080000000000000 35.251137130303420 + 1.2600000000000000 31.460882196188166 + 1.3120000000000001 27.952446089251964 + 1.3639999999999999 24.714743424808852 + 1.4159999999999999 21.736688818172937 + 1.4680000000000000 19.007196884658306 + 1.5200000000000000 16.515182239579076 + 1.5720000000000001 14.249559498249329 + 1.6240000000000001 12.199243275983154 + 1.6760000000000002 10.353148188094648 + 1.7280000000000000 8.7001888498979163 + 1.7800000000000000 7.2292798767070447 + 1.8320000000000001 5.9293358838361092 + 1.8839999999999999 4.7892714865992376 + 1.9359999999999999 3.7980013003104953 + 1.9880000000000000 2.9444399402839894 + 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+ 4.0999999999999996 2.0668142493140005E-002 + 4.2000000000000002 1.2430141080200409E-002 + 4.2999999999999998 7.2856566327403139E-003 + 4.3999999999999995 4.1560332011683883E-003 + 4.5000000000000000 2.3041281035584126E-003 + 4.5999999999999996 1.2397986929553748E-003 + 4.7000000000000002 6.4656516755885957E-004 + 4.7999999999999998 3.2635453161844339E-004 + 4.9000000000000004 1.5921458192287997E-004 + 5.0000000000000000 7.4970692168027886E-005 diff --git a/examples/README b/examples/README index 8f4cb0bd75..b563fd818e 100644 --- a/examples/README +++ b/examples/README @@ -189,6 +189,9 @@ corresponding doc page in the manual for more info. See the https://docs.lammps.org/Build_package.html page for more info about installing and building packages. +The QM directory has examples of how to use LAMMPS in tandem with +several quantum codes. + The TIP4P directory has an example for testing forces computed on a GPU. diff --git a/examples/mdi/LATTE/README b/examples/mdi/LATTE/README deleted file mode 100644 index 34c9e20330..0000000000 --- a/examples/mdi/LATTE/README +++ /dev/null @@ -1,63 +0,0 @@ -Examples in this directory use LAMMPS as an MDI driver code and the -LATTE tight-binding code as an MDI engine to perform ab initio MD and -evaluate the energy/forces/virial for a series of MD snapshots or -conformations with LATTE. - -Talk about LATTE package and fix latte command - ---------- - -copy lmp_mpi and LATTE_DOUBLE into this dir -LATTE always uses latte.in as input file, contains no element info - -this version of LATTE does not use MPI, only OpenMP or GPU -run LATTE with OpenMP: setenv OMP_NUM_THREADS max-core-count - ---------- - -Run AIMD test problem: - -build LAMMPS with molecule package -LAMMPS uses in.mdi.aimd or in.mdi.aimd.plugin - -++ Run with MPI: 1 proc each - -mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \ - -log log.aimd.driver.mpi.1 -in in.mdi.aimd : \ - -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI" - -++ Run with MPI: 2 procs for LAMMPS, 1 for LATTE - -mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \ - -log log.aimd.driver.mpi.1 -in in.mdi.aimd : \ - -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI" - -++ Run in plugin mode: 1 proc - -lmp_mpi -mdi \ - "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \ - -log log.aimd.driver.plugin.1 -in in.mdi.aimd.plugin - -mpirun -np 2 lmp_mpi -mdi \ - "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \ - -log log.aimd.driver.plugin.1 -in in.mdi.aimd.plugin - -++ Run with fix latte: 1 proc - -lmp_mpi < in.aimd - ---------- - -Run sequence of configs: - -++ Run with MPI: 1 proc each - -mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \ - -log log.series.driver.mpi.1 -in in.series.driver : \ - -np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI" - -++ Run in plugin mode: 1 proc - -lmp_mpi -mdi \ - "-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \ - -log log.series.driver.plugin.1 -in in.series.driver.plugin diff --git a/examples/mdi/README b/examples/mdi/README index 5f43f9df03..d6bcc48f21 100644 --- a/examples/mdi/README +++ b/examples/mdi/README @@ -2,6 +2,9 @@ These are examples that work the MDI package in LAMMPS which uses the MolSSI MDI library for coupling codes together and communicating between them with MDI messages. +There are more examples of using LAMMPS with quantum codes via MDI in +the examples/QM directory. + Within the MDI context, one code is the driver and another code is the engine. The 2 codes can be written in any language; C++ (LAMMPS) and Python are illustrated here. The 2 codes can each be stand-alone diff --git a/src/MDI/fix_mdi_qm.cpp b/src/MDI/fix_mdi_qm.cpp index d5e60c11e0..830ee18ffd 100644 --- a/src/MDI/fix_mdi_qm.cpp +++ b/src/MDI/fix_mdi_qm.cpp @@ -237,6 +237,7 @@ void FixMDIQM::init() } // send natoms, atom types or elements, and simulation box to engine + // confirm engine count of NATOMS is correct // this will trigger setup of a new system // subsequent calls in post_force() will be for same system until new init() @@ -245,36 +246,38 @@ void FixMDIQM::init() int natoms_exists; int ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &natoms_exists); if (ierr) error->all(FLERR, "MDI: >NATOMS command check"); - if ( natoms_exists ) { + MPI_Bcast(&natoms_exists, 1, MPI_INT, 0, world); + if (natoms_exists) { ierr = MDI_Send_command(">NATOMS", mdicomm); if (ierr) error->all(FLERR, "MDI: >NATOMS command"); int n = static_cast (atom->natoms); ierr = MDI_Send(&n, 1, MDI_INT, mdicomm); if (ierr) error->all(FLERR, "MDI: >NATOMS data"); - } else { // confirm that the engine's NATOMS is correct - + } else { ierr = MDI_Send_command("all(FLERR, "MDI: all(FLERR, "MDI: natoms ) error->all(FLERR, "MDI: Engine has the wrong number of atoms, and does not support the >NATOMS command."); + MPI_Bcast(&n, 1, MPI_INT, 0, world); + if (n != atom->natoms) error->all(FLERR, "MDI: Engine has wrong atom count and does not support >NATOMS command"); } int elements_exists; int types_exists; ierr = MDI_Check_command_exists("@DEFAULT", ">ELEMENTS", mdicomm, &elements_exists); if (ierr) error->all(FLERR, "MDI: >ELEMENTS command check"); + MPI_Bcast(&elements_exists, 1, MPI_INT, 0, world); + ierr = MDI_Check_command_exists("@DEFAULT", ">TYPES", mdicomm, &types_exists); if (ierr) error->all(FLERR, "MDI: >TYPES command check"); - if ( elements && elements_exists ) { - send_elements(); - } else if ( types_exists ) { - send_types(); - } + MPI_Bcast(&types_exists, 1, MPI_INT, 0, world); + + if (elements && elements_exists) send_elements(); + else if (types_exists) send_types(); send_box(); } @@ -530,7 +533,9 @@ void FixMDIQM::send_box() int celldispl_exists; int ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &celldispl_exists); if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command check"); - if ( celldispl_exists ) { + MPI_Bcast(&celldispl_exists, 1, MPI_INT, 0, world); + + if (celldispl_exists) { ierr = MDI_Send_command(">CELL_DISPL", mdicomm); if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command"); cell[0] = domain->boxlo[0] * lmp2mdi_length;