From 0ea2eabbb259849cb92e878f449a2fed669f01d8 Mon Sep 17 00:00:00 2001 From: Tom Swinburne Date: Fri, 17 Apr 2020 18:11:59 +0200 Subject: [PATCH] start of clean up --- .../Fe.eam.fs => misc/pafi/Fe_M07.eam.fs} | 0 examples/USER/{ => misc}/pafi/README | 3 +- .../pafi.lammps => misc/pafi/in.pafi.lammps} | 9 +- examples/USER/misc/pafi/log.pafi | 331 ++++ examples/USER/pafi/test.dat | 1391 ----------------- src/.gitignore | 3 + .../fix_hp.cpp => USER-MISC/fix_pafi.cpp} | 38 +- .../fix_hp.h => USER-MISC/fix_pafi.h} | 12 +- src/USER-PAFI/README | 12 - src/atom.cpp | 10 +- src/library.cpp | 11 + 11 files changed, 383 insertions(+), 1437 deletions(-) rename examples/USER/{pafi/Fe.eam.fs => misc/pafi/Fe_M07.eam.fs} (100%) rename examples/USER/{ => misc}/pafi/README (92%) rename examples/USER/{pafi/pafi.lammps => misc/pafi/in.pafi.lammps} (84%) create mode 100644 examples/USER/misc/pafi/log.pafi delete mode 100644 examples/USER/pafi/test.dat rename src/{USER-PAFI/fix_hp.cpp => USER-MISC/fix_pafi.cpp} (96%) rename src/{USER-PAFI/fix_hp.h => USER-MISC/fix_pafi.h} (93%) delete mode 100644 src/USER-PAFI/README diff --git a/examples/USER/pafi/Fe.eam.fs b/examples/USER/misc/pafi/Fe_M07.eam.fs similarity index 100% rename from examples/USER/pafi/Fe.eam.fs rename to examples/USER/misc/pafi/Fe_M07.eam.fs diff --git a/examples/USER/pafi/README b/examples/USER/misc/pafi/README similarity index 92% rename from examples/USER/pafi/README rename to examples/USER/misc/pafi/README index 762ae7c037..f79c0756a7 100644 --- a/examples/USER/pafi/README +++ b/examples/USER/misc/pafi/README @@ -26,6 +26,5 @@ make machine # for binary (machine= e.g. mpi) To run the example from this folder: ``` -mpirun -np NPROCS /path/to/lammps/src/lmp_machine < pafi.lammps +mpirun -np NPROCS /path/to/lammps/src/lmp_machine -in in.pafi.lammps ``` - diff --git a/examples/USER/pafi/pafi.lammps b/examples/USER/misc/pafi/in.pafi.lammps similarity index 84% rename from examples/USER/pafi/pafi.lammps rename to examples/USER/misc/pafi/in.pafi.lammps index aa07a036bc..63a14d96c4 100644 --- a/examples/USER/pafi/pafi.lammps +++ b/examples/USER/misc/pafi/in.pafi.lammps @@ -1,6 +1,7 @@ units metal - atom_style atomic +atom_modify map array sort 0 0.0 +neigh_modify every 2 delay 10 check yes page 1000000 one 100000 ## read in path data using fix property/atom fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz @@ -9,7 +10,8 @@ run 0 ## EAM potential pair_style eam/fs -pair_coeff * * ../Fe.eam.fs Fe +pair_coeff * * Fe_M07.eam.fs Fe + mass * 55.85 thermo 100 @@ -23,7 +25,7 @@ compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_dd run 0 ## fix name group-id hp compute-id temperature damp seed overdamped 0/1 com 0/1 -fix hp all hp pa 400.0 0.1 434 overdamped 1 com 1 +fix hp all pafi pa 1000.1 0.05 434 overdamped 1 com 1 run 0 variable dn equal f_hp[4]*f_hp[4] # should be zero fix af all ave/time 1 1000 1000 f_hp[1] f_hp[2] f_hp[3] v_dn @@ -46,3 +48,4 @@ unfix hp minimize 0 0 1000 1000 print "energy=${pe}" +write_data final.dat diff --git a/examples/USER/misc/pafi/log.pafi b/examples/USER/misc/pafi/log.pafi new file mode 100644 index 0000000000..c4d7a7daa1 --- /dev/null +++ b/examples/USER/misc/pafi/log.pafi @@ -0,0 +1,331 @@ +LAMMPS (19 Mar 2020) +units metal +boundary p p p +atom_style atomic + +## read in path data using fix property/atom +fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz +read_data test.dat fix pa NULL PafiPath + orthogonal box = (0 0 0) to (19.9872 19.9872 19.9872) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 687 atoms + read_data CPU = 0.00923154 secs +run 0 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:1950) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:166) +Per MPI rank memory allocation (min/avg/max) = 2.422 | 2.422 | 2.422 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 6.9535e-06 on 2 procs for 0 steps with 687 atoms + +107.9% CPU use with 2 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 +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 | | 6.954e-06 | | |100.00 + +Nlocal: 343.5 ave 353 max 334 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +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 +Neighbor list builds = 0 +Dangerous builds = 0 + +## EAM potential +pair_style eam/fs +pair_coeff * * Fe_M07.eam.fs Fe + +mass * 55.85 +thermo 100 + +compute pe all pe +variable pe equal pe +run 0 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.8 + ghost atom cutoff = 7.8 + binsize = 3.9, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam/fs, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.438 | 3.438 | 3.438 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -2828.1883 0 -2828.1883 3563.9872 +Loop time of 1.475e-06 on 2 procs for 0 steps with 687 atoms + +169.5% CPU use with 2 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 +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 | | 1.475e-06 | | |100.00 + +Nlocal: 343.5 ave 353 max 334 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 2474.5 ave 2484 max 2465 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 28898 ave 29188 max 28608 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 57796 +Ave neighs/atom = 84.1281 +Neighbor list builds = 0 +Dangerous builds = 0 +print "energy=${pe}" +energy=-2828.18833783692 + +## compute property/atom to access relevant fields +compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz +run 0 +Per MPI rank memory allocation (min/avg/max) = 3.438 | 3.438 | 3.438 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -2828.1883 0 -2828.1883 3563.9872 +Loop time of 1.683e-06 on 2 procs for 0 steps with 687 atoms + +208.0% CPU use with 2 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 +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 | | 1.683e-06 | | |100.00 + +Nlocal: 343.5 ave 353 max 334 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 2474.5 ave 2484 max 2465 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 28898 ave 29188 max 28608 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 57796 +Ave neighs/atom = 84.1281 +Neighbor list builds = 0 +Dangerous builds = 0 + +## fix name group-id hp compute-id temperature damp seed overdamped 0/1 com 0/1 +fix hp all hp pa 400.0 0.1 434 overdamped 1 com 1 +fix hp compute name,style: pa,property/atom +run 0 +Per MPI rank memory allocation (min/avg/max) = 4.938 | 4.938 | 4.938 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -2828.1883 0 -2828.1883 3563.9872 +Loop time of 2.206e-06 on 2 procs for 0 steps with 687 atoms + +294.7% CPU use with 2 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 +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 | | 2.206e-06 | | |100.00 + +Nlocal: 343.5 ave 353 max 334 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 2474.5 ave 2484 max 2465 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 28898 ave 29188 max 28608 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 57796 +Ave neighs/atom = 84.1281 +Neighbor list builds = 0 +Dangerous builds = 0 +variable dn equal f_hp[4]*f_hp[4] # should be zero +fix af all ave/time 1 1000 1000 f_hp[1] f_hp[2] f_hp[3] v_dn + +variable adn equal f_af[4] # should be zero +variable apf equal f_af[1] +run 1000 +Per MPI rank memory allocation (min/avg/max) = 4.938 | 4.938 | 4.938 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -2828.1883 0 -2828.1883 3563.9872 + 100 0 -2787.7125 0 -2787.7125 16811.138 + 200 0 -2787.3136 0 -2787.3136 17302.039 + 300 0 -2788.1621 0 -2788.1621 16576.307 + 400 0 -2791.1893 0 -2791.1893 15611.421 + 500 0 -2787.3835 0 -2787.3835 17015.601 + 600 0 -2791.3402 0 -2791.3402 13819.752 + 700 0 -2788.5604 0 -2788.5604 15661.073 + 800 0 -2788.26 0 -2788.26 15554.53 + 900 0 -2788.2513 0 -2788.2513 16693.47 + 1000 0 -2790.1726 0 -2790.1726 15862.893 +Loop time of 2.15129 on 2 procs for 1000 steps with 687 atoms + +Performance: 40.162 ns/day, 0.598 hours/ns, 464.837 timesteps/s +98.3% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9813 | 1.993 | 2.0047 | 0.8 | 92.64 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.058066 | 0.069807 | 0.081548 | 4.4 | 3.24 +Output | 0.00018995 | 0.0002629 | 0.00033584 | 0.0 | 0.01 +Modify | 0.081354 | 0.081403 | 0.081452 | 0.0 | 3.78 +Other | | 0.006816 | | | 0.32 + +Nlocal: 343.5 ave 353 max 334 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 2474.5 ave 2484 max 2465 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 28898 ave 29188 max 28608 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 57796 +Ave neighs/atom = 84.1281 +Neighbor list builds = 0 +Dangerous builds = 0 + +print "Squared displacement normal to hyperplane = ${adn} A^2" +Squared displacement normal to hyperplane = 1.92841033952627e-23 A^2 +print "average projected force = ${apf} eV/A" +average projected force = 0.303660991606611 eV/A +## minimize under same constraint (temperature effectively zero) +min_style fire + +minimize 0 0 1000 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:190) + Parameters for fire: + dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback + 0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes +Per MPI rank memory allocation (min/avg/max) = 4.938 | 4.938 | 4.938 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 0 -2790.1726 0 -2790.1726 15862.893 + 1100 0.01395318 -2828.1875 0 -2828.1862 3564.2791 + 1200 1.3924969e-08 -2828.1886 0 -2828.1886 3561.3085 + 1300 2.7246418e-10 -2828.1886 0 -2828.1886 3561.2517 + 1400 1.990932e-13 -2828.1886 0 -2828.1886 3561.2506 + 1500 3.6357963e-16 -2828.1886 0 -2828.1886 3561.2513 + 1600 3.7304413e-16 -2828.1886 0 -2828.1886 3561.252 + 1700 3.7758424e-16 -2828.1886 0 -2828.1886 3561.2527 + 1800 3.7938855e-16 -2828.1886 0 -2828.1886 3561.2534 + 1900 3.800255e-16 -2828.1886 0 -2828.1886 3561.2542 + 2000 3.8025411e-16 -2828.1886 0 -2828.1886 3561.2549 +Loop time of 1.14675 on 2 procs for 1000 steps with 687 atoms + +97.6% CPU use with 2 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -2790.17255859 -2828.18861166 -2828.18861166 + Force two-norm initial, final = 27.9307 5.03831e-07 + Force max component initial, final = 2.89389 1.97794e-07 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 1000 1018 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0279 | 1.0557 | 1.0836 | 2.7 | 92.06 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.034238 | 0.062094 | 0.089951 | 11.2 | 5.41 +Output | 0.00014876 | 0.00019727 | 0.00024578 | 0.0 | 0.02 +Modify | 0.017477 | 0.017529 | 0.01758 | 0.0 | 1.53 +Other | | 0.01121 | | | 0.98 + +Nlocal: 343.5 ave 345 max 342 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 2474.5 ave 2476 max 2473 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 28901.5 ave 30125 max 27678 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 57803 +Ave neighs/atom = 84.1383 +Neighbor list builds = 0 +Dangerous builds = 0 +print "energy=${pe}" +energy=-2828.1886116623 + +## minimize without constraint +unfix af +unfix hp +minimize 0 0 1000 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:190) + Parameters for fire: + dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback + 0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes +Per MPI rank memory allocation (min/avg/max) = 4.563 | 4.563 | 4.563 Mbytes +Step Temp E_pair E_mol TotEng Press + 2000 0 -2828.1886 0 -2828.1886 3561.2549 + 2100 0.00019671788 -2828.3784 0 -2828.3784 3831.5695 + 2200 1.3047007e-08 -2828.3785 0 -2828.3785 3828.431 + 2300 1.2837148e-11 -2828.3785 0 -2828.3785 3828.4076 + 2400 3.6777219e-16 -2828.3785 0 -2828.3785 3828.4068 + 2500 1.0710252e-18 -2828.3785 0 -2828.3785 3828.4068 + 2600 1.3523987e-23 -2828.3785 0 -2828.3785 3828.4068 + 2700 1.4824109e-25 -2828.3785 0 -2828.3785 3828.4068 + 2800 2.3789827e-26 -2828.3785 0 -2828.3785 3828.4068 + 2900 1.6175585e-25 -2828.3785 0 -2828.3785 3828.4068 + 3000 2.6404401e-26 -2828.3785 0 -2828.3785 3828.4068 +Loop time of 1.0043 on 2 procs for 1000 steps with 687 atoms + +97.4% CPU use with 2 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -2828.18861166 -2828.37851625 -2828.37851625 + Force two-norm initial, final = 0.380384 3.56702e-13 + Force max component initial, final = 0.149002 3.48055e-14 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 1000 1029 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.93605 | 0.94701 | 0.95796 | 1.1 | 94.30 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.034637 | 0.04556 | 0.056484 | 5.1 | 4.54 +Output | 0.00014805 | 0.00019121 | 0.00023438 | 0.0 | 0.02 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.01154 | | | 1.15 + +Nlocal: 343.5 ave 353 max 334 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 2474.5 ave 2484 max 2465 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 28898.5 ave 29188 max 28609 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 57797 +Ave neighs/atom = 84.1295 +Neighbor list builds = 0 +Dangerous builds = 0 +print "energy=${pe}" +energy=-2828.37851624648 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/USER/pafi/test.dat b/examples/USER/pafi/test.dat deleted file mode 100644 index 78f3b4e446..0000000000 --- a/examples/USER/pafi/test.dat +++ /dev/null @@ -1,1391 +0,0 @@ -# USER-PAFI test data - -687 atoms -1 atom types - -0.0000000000000000e+00 1.9987183999999999e+01 xlo xhi -0.0000000000000000e+00 1.9987183999999999e+01 ylo yhi -0.0000000000000000e+00 1.9987183999999999e+01 zlo zhi - -Masses - -1 55.85 - -Atoms - -1 1 0.00528407 0.00391426 8.11661e-05 -2 1 1.42764 1.42466 1.42317 -3 1 2.85714 -0.000255876 -0.00153 -4 1 4.28079 1.42345 1.42477 -5 1 5.70926 0.000158292 0.000358096 -6 1 7.13582 1.42509 1.426 -7 1 8.56295 0.00210881 0.00191953 -8 1 9.9915 1.42684 1.42641 -9 1 11.4186 0.00381771 0.00257888 -10 1 12.848 1.42809 1.42614 -11 1 14.2762 0.00527717 0.00264919 -12 1 15.7058 1.42859 1.42522 -13 1 17.1355 0.00606398 0.00212618 -14 1 18.5637 1.42741 1.42356 -15 1 -0.000150615 2.85343 19.983 -16 1 1.42393 4.27658 1.42232 -17 1 2.85251 2.85039 19.9849 -18 1 4.27748 4.27589 1.424 -19 1 5.70805 2.85119 19.9869 -20 1 7.13536 4.2786 1.42615 -21 1 8.56425 2.85332 19.9874 -22 1 9.99214 4.28064 1.42653 -23 1 11.4201 2.85464 19.9872 -24 1 12.8485 4.28099 1.42598 -25 1 14.2764 2.85503 19.9865 -26 1 15.7066 4.27941 1.42359 -27 1 17.1335 2.85444 19.9846 -28 1 18.561 4.27939 1.42235 -29 1 -0.000711408 5.70629 19.9844 -30 1 1.42445 7.13388 1.42369 -31 1 2.85033 5.70508 19.9866 -32 1 4.27723 7.13388 1.42567 -33 1 5.70585 5.70544 19.9891 -34 1 7.1339 7.13458 1.42812 -35 1 8.56379 5.70818 19.9894 -36 1 9.99191 7.13715 1.42913 -37 1 11.4204 5.70946 19.9886 -38 1 12.8493 7.13633 1.42737 -39 1 14.2769 5.70883 19.9871 -40 1 15.7055 7.13629 1.42459 -41 1 17.1318 5.70888 19.9846 -42 1 18.5617 7.13458 1.42349 -43 1 0.000947509 8.56274 19.9868 -44 1 1.42618 9.99293 1.42538 -45 1 2.85104 8.56344 19.9883 -46 1 4.27901 9.99308 1.42737 -47 1 5.70602 8.56339 19.9903 -48 1 7.13597 9.9917 1.42997 -49 1 8.56328 8.56429 19.9895 -50 1 9.99254 9.99129 1.43063 -51 1 11.4205 8.56557 19.9886 -52 1 12.8485 9.99351 1.42898 -53 1 14.2755 8.5662 19.9879 -54 1 15.7064 9.99332 1.42624 -55 1 17.1336 8.56352 19.9877 -56 1 18.5631 9.99238 1.42502 -57 1 0.0028007 11.4213 0.00166032 -58 1 1.42829 12.8517 1.42696 -59 1 2.85256 11.4223 0.00227196 -60 1 4.28147 12.8505 1.42894 -61 1 5.70738 11.4214 0.00406528 -62 1 7.13791 12.8478 1.4306 -63 1 8.56439 11.4205 0.00292891 -64 1 9.9936 12.8467 1.4311 -65 1 11.4209 11.4216 0.00186068 -66 1 12.8492 12.85 1.42978 -67 1 14.2777 11.4221 0.00200513 -68 1 15.7072 12.8514 1.42744 -69 1 17.1357 11.4212 0.0027393 -70 1 18.5644 12.8515 1.42638 -71 1 0.00470877 14.2804 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18.5669 -0.00112416 0.000422696 8.59973e-05 -0.00286298 -0.00473802 -0.00387171 -681 11.4142 17.149 17.1498 -0.00179607 0.000964405 0.00104077 -0.00542361 -0.00642182 -0.0066187 -682 12.8469 18.5696 18.5688 -0.00011424 0.000659006 0.00038274 -0.00680772 -0.00554022 -0.00439037 -683 14.2843 17.1553 17.156 3.36173e-05 0.00189075 0.00201196 -0.0103955 -0.00781061 -0.00703611 -684 15.7095 18.5724 18.5703 0.00112776 0.000930463 0.000421995 -0.00878223 -0.00614574 -0.0038771 -685 17.1546 17.157 17.1559 0.00319802 0.00242263 0.00223538 -0.00908754 -0.00595537 -0.00276044 -686 18.57 18.5717 18.5686 0.00198459 0.0010239 0.000169766 -0.00600572 -0.00563487 -0.00214845 -687 10.4921 10.683 11.2164 0.328595 -0.0571837 0.384537 -0.123219 0.0413041 -0.0278179 diff --git a/src/.gitignore b/src/.gitignore index fabd3b4e4b..d879bb120c 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -59,6 +59,9 @@ /fix_*cauchy.cpp /fix_*cauchy.h +/fix_pafi*.cpp +/fix_pafi*.h + /compute_test_nbl.cpp /compute_test_nbl.h /pair_multi_lucy.cpp diff --git a/src/USER-PAFI/fix_hp.cpp b/src/USER-MISC/fix_pafi.cpp similarity index 96% rename from src/USER-PAFI/fix_hp.cpp rename to src/USER-MISC/fix_pafi.cpp index ec742f1f85..8e47f14441 100644 --- a/src/USER-PAFI/fix_hp.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -22,7 +22,7 @@ #include #include #include -#include "fix_hp.h" +#include "fix_pafi.h" #include "math_extra.h" #include "atom.h" #include "force.h" @@ -66,7 +66,7 @@ enum{NONE,CONSTANT,EQUAL,ATOM}; /* ---------------------------------------------------------------------- */ -FixHP::FixHP(LAMMPS *lmp, int narg, char **arg) : +FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), idregion(NULL), random(NULL) { if (lmp->citeme) lmp->citeme->add(cite_user_pafi_package); @@ -156,7 +156,7 @@ FixHP::FixHP(LAMMPS *lmp, int narg, char **arg) : results_all[i] = 0.0; } maxatom = 1; - memory->create(h,maxatom,3,"fixhp:h"); + memory->create(h,maxatom,3,"FixPAFI:h"); // initialize Marsaglia RNG with processor-unique seed random = new RanMars(lmp,seed + comm->me); @@ -168,7 +168,7 @@ FixHP::FixHP(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -FixHP::~FixHP() +FixPAFI::~FixPAFI() { if (copymode) return; delete random; @@ -178,7 +178,7 @@ FixHP::~FixHP() /* ---------------------------------------------------------------------- */ -int FixHP::setmask() +int FixPAFI::setmask() { int mask = 0; mask |= POST_FORCE; @@ -194,7 +194,7 @@ int FixHP::setmask() /* ---------------------------------------------------------------------- */ -void FixHP::init() +void FixPAFI::init() { // set index and check validity of region // nve @@ -216,7 +216,7 @@ void FixHP::init() } -void FixHP::setup(int vflag) +void FixPAFI::setup(int vflag) { if (strstr(update->integrate_style,"verlet")) post_force(vflag); @@ -228,7 +228,7 @@ void FixHP::setup(int vflag) } } -void FixHP::min_setup(int vflag) +void FixPAFI::min_setup(int vflag) { if( strcmp(update->minimize_style,"fire")!=0 && strcmp(update->minimize_style,"quickmin")!=0 ) error->all(FLERR,"fix hp requires damped dynamics minimizer"); @@ -236,7 +236,7 @@ void FixHP::min_setup(int vflag) } -void FixHP::post_force(int vflag) +void FixPAFI::post_force(int vflag) { double **x = atom->x; double **v = atom->v; @@ -257,7 +257,7 @@ void FixHP::post_force(int vflag) if (atom->nmax > maxatom) { maxatom = atom->nmax; memory->destroy(h); - memory->create(h,maxatom,3,"fixhp:h"); + memory->create(h,maxatom,3,"FixPAFI:h"); } PathCompute->compute_peratom(); @@ -410,7 +410,7 @@ void FixHP::post_force(int vflag) }; -void FixHP::post_force_respa(int vflag, int ilevel, int iloop) +void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop) { // set force to desired value on requested level, 0.0 on other levels @@ -434,7 +434,7 @@ void FixHP::post_force_respa(int vflag, int ilevel, int iloop) } }; -void FixHP::min_post_force(int vflag) +void FixPAFI::min_post_force(int vflag) { double **x = atom->x; double **v = atom->v; @@ -559,14 +559,14 @@ void FixHP::min_post_force(int vflag) } }; -double FixHP::compute_vector(int n) +double FixPAFI::compute_vector(int n) { return results_all[n]; }; -void FixHP::initial_integrate(int vflag) +void FixPAFI::initial_integrate(int vflag) { double dtfm; @@ -681,7 +681,7 @@ void FixHP::initial_integrate(int vflag) /* ---------------------------------------------------------------------- */ -void FixHP::final_integrate() +void FixPAFI::final_integrate() { double dtfm; @@ -757,7 +757,7 @@ void FixHP::final_integrate() /* ---------------------------------------------------------------------- */ -void FixHP::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int iloop) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -771,7 +771,7 @@ void FixHP::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixHP::final_integrate_respa(int ilevel, int iloop) +void FixPAFI::final_integrate_respa(int ilevel, int iloop) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); @@ -779,7 +779,7 @@ void FixHP::final_integrate_respa(int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixHP::reset_dt() +void FixPAFI::reset_dt() { dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; @@ -790,7 +790,7 @@ void FixHP::reset_dt() memory usage of local atom-based array ------------------------------------------------------------------------- */ -double FixHP::memory_usage() +double FixPAFI::memory_usage() { double bytes = 0.0; bytes = maxatom*3 * sizeof(double); diff --git a/src/USER-PAFI/fix_hp.h b/src/USER-MISC/fix_pafi.h similarity index 93% rename from src/USER-PAFI/fix_hp.h rename to src/USER-MISC/fix_pafi.h index 9eeed86e99..0839c68c46 100644 --- a/src/USER-PAFI/fix_hp.h +++ b/src/USER-MISC/fix_pafi.h @@ -13,22 +13,22 @@ #ifdef FIX_CLASS -FixStyle(hp,FixHP) +FixStyle(pafi,FixPAFI) #else -#ifndef LMP_FIX_HP_H -#define LMP_FIX_HP_H +#ifndef LMP_FIX_PAFI_H +#define LMP_FIX_PAFI_H #include "fix.h" #include "compute.h" namespace LAMMPS_NS { -class FixHP : public Fix { +class FixPAFI : public Fix { public: - FixHP(class LAMMPS *, int, char **); - virtual ~FixHP(); + FixPAFI(class LAMMPS *, int, char **); + virtual ~FixPAFI(); int setmask(); virtual void init(); diff --git a/src/USER-PAFI/README b/src/USER-PAFI/README deleted file mode 100644 index 7e7127b27c..0000000000 --- a/src/USER-PAFI/README +++ /dev/null @@ -1,12 +0,0 @@ - -LAMMPS package for PAFI = (Projected Average Force Integrator) -author: -Thomas D Swinburne -CNRS / CINaM Marseille -swinburne at cinam.univ-mrs.fr -tomswinburne.github.io - -Code used in https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.135503 -Unsupervised Calculation of Free Energy Barriers in Large Crystalline Systems -T.D. Swinburne and M.-C. Marinica -Physical Review Letters 120 (13), 135503, 2018 diff --git a/src/atom.cpp b/src/atom.cpp index 90e801d655..5a3bd4387a 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -2294,11 +2294,13 @@ void *Atom::extract(char *name) if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta; if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp; - // when used with fix property/atom - int cf=0; - int idv = find_custom(name, cf); - if(idv>=0) return (void *) dvector[idv]; + int vector_index, vector_type; + vector_index = lmp->atom->find_custom(name, vector_type); + if(vector_index>=0) return (void *) dvector[vector_index]; + + + return NULL; } diff --git a/src/library.cpp b/src/library.cpp index 5274d0058e..c5cc260bf5 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -831,6 +831,17 @@ void lammps_gather_atoms(void *ptr, char *name, int natoms = static_cast (lmp->atom->natoms); void *vptr = lmp->atom->extract(name); + + // look for property/atom if NULL + /*int vector_index, vector_type=type; + if (vptr == NULL) { + vector_index = lmp->atom->find_custom(name, vector_type); + if(vector_index>=0 && vector_type == type) { + if(type==0) vptr = (void *) lmp->atom->ivector[vector_index]; + else vptr = (void *) lmp->atom->dvector[vector_index]; + } + }*/ + if (vptr == NULL) { lmp->error->warning(FLERR,"lammps_gather_atoms: unknown property name"); return;