From 33b64666115f1298847f0ff2389aa88c92cb87a9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 31 Mar 2022 07:31:43 -0400 Subject: [PATCH] add minimal fix tmd example --- examples/PACKAGES/tmd/data.peptide | 1 + examples/PACKAGES/tmd/in.tmd | 45 ++++ examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1 | 210 ++++++++++++++++++ examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4 | 210 ++++++++++++++++++ .../PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1 | 4 + .../PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4 | 4 + examples/PACKAGES/tmd/tmd.target | 13 ++ 7 files changed, 487 insertions(+) create mode 120000 examples/PACKAGES/tmd/data.peptide create mode 100644 examples/PACKAGES/tmd/in.tmd create mode 100644 examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1 create mode 100644 examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4 create mode 100644 examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1 create mode 100644 examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4 create mode 100644 examples/PACKAGES/tmd/tmd.target diff --git a/examples/PACKAGES/tmd/data.peptide b/examples/PACKAGES/tmd/data.peptide new file mode 120000 index 0000000000..47dd25a04b --- /dev/null +++ b/examples/PACKAGES/tmd/data.peptide @@ -0,0 +1 @@ +../../peptide/data.peptide \ No newline at end of file diff --git a/examples/PACKAGES/tmd/in.tmd b/examples/PACKAGES/tmd/in.tmd new file mode 100644 index 0000000000..6cbf57b951 --- /dev/null +++ b/examples/PACKAGES/tmd/in.tmd @@ -0,0 +1,45 @@ +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style multi +thermo 50 + +group tmd id 1:6 + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 +fix 0 tmd tmd 0.1 tmd.target 100 tmd.log +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + +group peptide type <= 12 + +#dump 1 peptide atom 10 dump.peptide + +#dump 2 peptide image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 2 pad 3 + +#dump 3 peptide movie 25 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 3 pad 3 + +#compute bnd all property/local btype batom1 batom2 +#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3] + +run 300 + diff --git a/examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1 b/examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1 new file mode 100644 index 0000000000..ff290e55c6 --- /dev/null +++ b/examples/PACKAGES/tmd/log.31Mar22.tmd.g++.1 @@ -0,0 +1,210 @@ +LAMMPS (24 Mar 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide +Reading data file ... + orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.011 seconds + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style multi +thermo 50 + +group tmd id 1:6 +6 atoms in group tmd + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 +fix 0 tmd tmd 0.1 tmd.target 100 tmd.log +Reading TMD target file tmd.target ... +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + find clusters CPU = 0.000 seconds + +group peptide type <= 12 +84 atoms in group peptide + +#dump 1 peptide atom 10 dump.peptide + +#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 2 pad 3 + +#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 3 pad 3 + +#compute bnd all property/local btype batom1 batom2 +#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3] + +run 300 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:340) + G vector (1/distance) = 0.26872465 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.022820853 + estimated relative force accuracy = 6.872432e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 10648 3375 + generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +SHAKE stats (type/ave/delta/count) on step 0 +Bond: 4 1.111 1.44264e-05 9 +Bond: 6 0.996998 7.26967e-06 6 +Bond: 8 1.08 1.32536e-05 9 +Bond: 10 1.111 1.22749e-05 8 +Bond: 12 1.08 1.11767e-05 9 +Bond: 14 0.96 0 1 +Bond: 18 0.957206 4.37979e-05 1280 +Angle: 31 104.519 0.00396029 640 +Per MPI rank memory allocation (min/avg/max) = 19.78 | 19.78 | 19.78 Mbytes +------------ Step 0 ----- CPU = 0 (sec) ------------- +TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 +PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 +E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 +E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 +------------ Step 50 ----- CPU = 0.6301453 (sec) ------------- +TotEng = -5001.6799 KinEng = 1319.3760 Temp = 327.9501 +PotEng = -6321.0559 E_bond = 17.4415 E_angle = 42.4509 +E_dihed = 25.0839 E_impro = 4.4025 E_vdwl = 725.7619 +E_coul = 26771.0015 E_long = -33907.1980 Press = -1.1409 +SHAKE stats (type/ave/delta/count) on step 100 +Bond: 4 1.11096 0.000146572 9 +Bond: 6 0.996997 7.55911e-06 6 +Bond: 8 1.08 8.22449e-06 9 +Bond: 10 1.11099 3.00424e-05 8 +Bond: 12 1.08 6.53505e-06 9 +Bond: 14 0.95999 0 1 +Bond: 18 0.957195 4.74892e-05 1280 +Angle: 31 104.52 0.00446577 640 +------------ Step 100 ----- CPU = 1.251267 (sec) ------------- +TotEng = -5114.3221 KinEng = 1168.2996 Temp = 290.3979 +PotEng = -6282.6217 E_bond = 45.5470 E_angle = 87.5725 +E_dihed = 26.1332 E_impro = 1.8662 E_vdwl = 791.5291 +E_coul = 26670.6791 E_long = -33905.9488 Press = -29.3446 +------------ Step 150 ----- CPU = 1.869158 (sec) ------------- +TotEng = -5302.3058 KinEng = 1211.4300 Temp = 301.1186 +PotEng = -6513.7358 E_bond = 51.4069 E_angle = 82.5752 +E_dihed = 31.1298 E_impro = 4.3390 E_vdwl = 764.0550 +E_coul = 26461.8974 E_long = -33909.1392 Press = -1204.2714 +SHAKE stats (type/ave/delta/count) on step 200 +Bond: 4 1.11094 0.000292869 9 +Bond: 6 0.996989 3.13206e-05 6 +Bond: 8 1.07999 4.4723e-05 9 +Bond: 10 1.111 1.08895e-05 8 +Bond: 12 1.07999 1.42694e-05 9 +Bond: 14 0.959976 0 1 +Bond: 18 0.957195 8.58256e-05 1280 +Angle: 31 104.52 0.00597861 640 +------------ Step 200 ----- CPU = 2.48933 (sec) ------------- +TotEng = -5785.4658 KinEng = 1048.7220 Temp = 260.6751 +PotEng = -6834.1879 E_bond = 21.7304 E_angle = 48.3249 +E_dihed = 20.5973 E_impro = 2.0603 E_vdwl = 818.9175 +E_coul = 26165.9672 E_long = -33911.7854 Press = -1228.5741 +------------ Step 250 ----- CPU = 3.119859 (sec) ------------- +TotEng = -6108.4578 KinEng = 828.5247 Temp = 205.9419 +PotEng = -6936.9825 E_bond = 26.5971 E_angle = 68.2771 +E_dihed = 36.1232 E_impro = 5.2092 E_vdwl = 884.1147 +E_coul = 25955.7300 E_long = -33913.0338 Press = -1365.4744 +SHAKE stats (type/ave/delta/count) on step 300 +Bond: 4 1.11174 0.0109853 9 +Bond: 6 0.996999 1.94772e-06 6 +Bond: 8 1.08 3.97091e-06 9 +Bond: 10 1.111 2.52635e-06 8 +Bond: 12 1.08 1.24444e-06 9 +Bond: 14 0.96 0 1 +Bond: 18 0.9572 1.22873e-05 1280 +Angle: 31 104.52 0.00134864 640 +------------ Step 300 ----- CPU = 3.74524 (sec) ------------- +TotEng = -5492.5012 KinEng = 1315.6902 Temp = 327.0339 +PotEng = -6808.1914 E_bond = 88.7967 E_angle = 104.4231 +E_dihed = 28.2383 E_impro = 43.5062 E_vdwl = 992.5311 +E_coul = 25849.1502 E_long = -33914.8370 Press = 268.8004 +Loop time of 3.74527 on 1 procs for 300 steps with 2004 atoms + +Performance: 13.841 ns/day, 1.734 hours/ns, 80.101 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.9399 | 2.9399 | 2.9399 | 0.0 | 78.50 +Bond | 0.0069522 | 0.0069522 | 0.0069522 | 0.0 | 0.19 +Kspace | 0.25203 | 0.25203 | 0.25203 | 0.0 | 6.73 +Neigh | 0.48624 | 0.48624 | 0.48624 | 0.0 | 12.98 +Comm | 0.016948 | 0.016948 | 0.016948 | 0.0 | 0.45 +Output | 0.00023689 | 0.00023689 | 0.00023689 | 0.0 | 0.01 +Modify | 0.039476 | 0.039476 | 0.039476 | 0.0 | 1.05 +Other | | 0.003502 | | | 0.09 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11242 ave 11242 max 11242 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 710782 ave 710782 max 710782 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 710782 +Ave neighs/atom = 354.68164 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 32 +Dangerous builds = 1 + +Total wall time: 0:00:03 diff --git a/examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4 b/examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4 new file mode 100644 index 0000000000..c38f5ae7bb --- /dev/null +++ b/examples/PACKAGES/tmd/log.31Mar22.tmd.g++.4 @@ -0,0 +1,210 @@ +LAMMPS (24 Mar 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide +Reading data file ... + orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.017 seconds + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style multi +thermo 50 + +group tmd id 1:6 +6 atoms in group tmd + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 +fix 0 tmd tmd 0.1 tmd.target 100 tmd.log +Reading TMD target file tmd.target ... +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + find clusters CPU = 0.000 seconds + +group peptide type <= 12 +84 atoms in group peptide + +#dump 1 peptide atom 10 dump.peptide + +#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 2 pad 3 + +#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5 +#dump_modify 3 pad 3 + +#compute bnd all property/local btype batom1 batom2 +#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3] + +run 300 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:340) + G vector (1/distance) = 0.26872465 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.022820853 + estimated relative force accuracy = 6.872432e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 4312 960 + generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +SHAKE stats (type/ave/delta/count) on step 0 +Bond: 4 1.111 1.44264e-05 9 +Bond: 6 0.996998 7.26967e-06 6 +Bond: 8 1.08 1.32536e-05 6 +Bond: 10 1.111 1.22749e-05 8 +Bond: 12 1.08 1.11767e-05 9 +Bond: 14 0.96 0 1 +Bond: 18 0.957206 4.37979e-05 1280 +Angle: 31 104.519 0.00396029 640 +Per MPI rank memory allocation (min/avg/max) = 16.78 | 16.97 | 17.16 Mbytes +------------ Step 0 ----- CPU = 0 (sec) ------------- +TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 +PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 +E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 +E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 +------------ Step 50 ----- CPU = 0.1916178 (sec) ------------- +TotEng = -5001.6799 KinEng = 1319.3760 Temp = 327.9501 +PotEng = -6321.0559 E_bond = 17.4415 E_angle = 42.4509 +E_dihed = 25.0839 E_impro = 4.4025 E_vdwl = 725.7619 +E_coul = 26771.0015 E_long = -33907.1980 Press = -1.1409 +SHAKE stats (type/ave/delta/count) on step 100 +Bond: 4 1.11096 0.000146572 9 +Bond: 6 0.996997 7.55911e-06 6 +Bond: 8 1.08 8.22449e-06 6 +Bond: 10 1.11099 3.00424e-05 8 +Bond: 12 1.08 6.53505e-06 9 +Bond: 14 0.95999 0 1 +Bond: 18 0.957195 4.74892e-05 1280 +Angle: 31 104.52 0.00446577 640 +------------ Step 100 ----- CPU = 0.3672111 (sec) ------------- +TotEng = -5114.3221 KinEng = 1168.2996 Temp = 290.3979 +PotEng = -6282.6217 E_bond = 45.5470 E_angle = 87.5725 +E_dihed = 26.1332 E_impro = 1.8662 E_vdwl = 791.5291 +E_coul = 26670.6792 E_long = -33905.9488 Press = -29.3446 +------------ Step 150 ----- CPU = 0.5543252 (sec) ------------- +TotEng = -5302.3058 KinEng = 1211.4300 Temp = 301.1186 +PotEng = -6513.7358 E_bond = 51.4069 E_angle = 82.5752 +E_dihed = 31.1298 E_impro = 4.3390 E_vdwl = 764.0550 +E_coul = 26461.8975 E_long = -33909.1392 Press = -1204.2714 +SHAKE stats (type/ave/delta/count) on step 200 +Bond: 4 1.11094 0.000292869 9 +Bond: 6 0.996989 3.13206e-05 6 +Bond: 8 1.07999 4.4723e-05 6 +Bond: 10 1.111 1.08895e-05 8 +Bond: 12 1.07999 1.42694e-05 9 +Bond: 14 0.959976 0 1 +Bond: 18 0.957195 8.58257e-05 1280 +Angle: 31 104.52 0.00597861 640 +------------ Step 200 ----- CPU = 0.7449468 (sec) ------------- +TotEng = -5785.4658 KinEng = 1048.7220 Temp = 260.6751 +PotEng = -6834.1878 E_bond = 21.7304 E_angle = 48.3249 +E_dihed = 20.5973 E_impro = 2.0603 E_vdwl = 818.9173 +E_coul = 26165.9673 E_long = -33911.7854 Press = -1228.5754 +------------ Step 250 ----- CPU = 0.9417257 (sec) ------------- +TotEng = -6108.4577 KinEng = 828.5246 Temp = 205.9418 +PotEng = -6936.9823 E_bond = 26.5971 E_angle = 68.2771 +E_dihed = 36.1232 E_impro = 5.2092 E_vdwl = 884.1146 +E_coul = 25955.7302 E_long = -33913.0338 Press = -1365.4736 +SHAKE stats (type/ave/delta/count) on step 300 +Bond: 4 1.11174 0.0109854 9 +Bond: 6 0.996999 1.94775e-06 6 +Bond: 8 1.08 3.97089e-06 6 +Bond: 10 1.111 2.52634e-06 8 +Bond: 12 1.08 1.24445e-06 9 +Bond: 14 0.96 0 1 +Bond: 18 0.9572 1.22873e-05 1280 +Angle: 31 104.52 0.0013486 640 +------------ Step 300 ----- CPU = 1.137003 (sec) ------------- +TotEng = -5492.5016 KinEng = 1315.6899 Temp = 327.0339 +PotEng = -6808.1915 E_bond = 88.7968 E_angle = 104.4228 +E_dihed = 28.2384 E_impro = 43.5061 E_vdwl = 992.5315 +E_coul = 25849.1499 E_long = -33914.8370 Press = 268.8010 +Loop time of 1.13706 on 4 procs for 300 steps with 2004 atoms + +Performance: 45.591 ns/day, 0.526 hours/ns, 263.838 timesteps/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.75407 | 0.80373 | 0.84144 | 3.6 | 70.68 +Bond | 0.0010088 | 0.0024668 | 0.0045274 | 2.6 | 0.22 +Kspace | 0.095468 | 0.13434 | 0.18276 | 8.9 | 11.81 +Neigh | 0.13509 | 0.13515 | 0.13522 | 0.0 | 11.89 +Comm | 0.024217 | 0.025086 | 0.026404 | 0.5 | 2.21 +Output | 0.00020952 | 0.00023591 | 0.00031389 | 0.0 | 0.02 +Modify | 0.033319 | 0.033374 | 0.033436 | 0.0 | 2.94 +Other | | 0.00268 | | | 0.24 + +Nlocal: 501 ave 530 max 459 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Nghost: 6562.75 ave 6755 max 6370 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 177696 ave 195050 max 158403 min +Histogram: 1 0 0 1 0 0 0 1 0 1 + +Total # of neighbors = 710782 +Ave neighs/atom = 354.68164 +Ave special neighs/atom = 2.3403194 +Neighbor list builds = 32 +Dangerous builds = 1 + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1 b/examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1 new file mode 100644 index 0000000000..6b1732cb2a --- /dev/null +++ b/examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.1 @@ -0,0 +1,4 @@ +# Step rho_target rho_old gamma_back gamma_forward lambda work_lambda work_analytical +100 11.580338717125848 11.637740410711476 0.00432656530431019 -0.0006058453921097923 1295.0393774041895 -7808.460018545273 562.4687334224966 +200 5.840169358562925 5.897571052148553 0.009256742629063092 -0.0004765379201060169 1404.114149312145 -15441.509720360129 1352.9255849946983 +300 0.10000000000000142 0.15740169358562994 -0.030035833473071705 -0.5643261296323345 -121.59623659080042 -22929.738462520727 2299.6676396746325 diff --git a/examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4 b/examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4 new file mode 100644 index 0000000000..17188a756a --- /dev/null +++ b/examples/PACKAGES/tmd/tmd.log.31Mar22.tmd.g++.4 @@ -0,0 +1,4 @@ +# Step rho_target rho_old gamma_back gamma_forward lambda work_lambda work_analytical +100 11.580338717125848 11.637740410711476 0.004326565303381905 -0.0006058453930379918 1295.0393771263327 -7808.46001855425 562.4687334073235 +200 5.840169358562925 5.897571052148553 0.009256742652188668 -0.0004765378969710561 1404.114152819961 -15441.50972264099 1352.9255825827688 +300 0.10000000000000142 0.15740169358562994 -0.03003651537895091 -0.5643268572640833 -121.59899719968097 -22929.73877163682 2299.6674130478946 diff --git a/examples/PACKAGES/tmd/tmd.target b/examples/PACKAGES/tmd/tmd.target new file mode 100644 index 0000000000..e83cebb32c --- /dev/null +++ b/examples/PACKAGES/tmd/tmd.target @@ -0,0 +1,13 @@ +# pull a few peptide atoms across the box + 36.840194 64.211560 xlo xhi + 41.013691 68.385058 ylo yhi + 29.768095 57.139462 zlo zhi # comment +# comment + 1 53.99993 48.52678 46.78550 0 0 0 + 2 55.10395 48.23499 45.86693 0 0 0 + 3 53.81519 49.54928 47.43995 0 0 0 + 4 55.71714 47.34797 46.13434 0 0 0 + 5 55.72261 49.13657 45.67007 0 0 0 + 6 54.66624 48.09539 44.85538 0 0 0 + 7 53.28193 47.47427 46.91953 0 0 0 + 8 52.07157 47.45486 47.62418 0 0 0