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add minimal fix tmd example

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Axel Kohlmeyer
2022-03-31 07:31:43 -04:00
parent b97c30e6e7
commit 33b6466611
7 changed files with 487 additions and 0 deletions
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examples/PACKAGES/tmd/data.peptide Symbolic link
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../../peptide/data.peptide

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examples/PACKAGES/tmd/in.tmd Normal file
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# 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

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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

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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

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# 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

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# 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

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# 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