Merge branch 'develop' into ctip
This commit is contained in:
Axel Kohlmeyer
@ -41,7 +41,6 @@
|
||||
|
||||
#include <stdlib.h>
|
||||
|
||||
|
||||
liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
{
|
||||
liblammpsplugin_t *lmp;
|
||||
@ -101,9 +100,12 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(extract_setting);
|
||||
ADDSYM(extract_global_datatype);
|
||||
ADDSYM(extract_global);
|
||||
ADDSYM(extract_pair_dimension);
|
||||
ADDSYM(extract_pair);
|
||||
ADDSYM(map_atom);
|
||||
|
||||
ADDSYM(extract_atom_datatype);
|
||||
ADDSYM(extract_atom_size);
|
||||
ADDSYM(extract_atom);
|
||||
|
||||
ADDSYM(extract_compute);
|
||||
@ -148,6 +150,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(config_has_png_support);
|
||||
ADDSYM(config_has_jpeg_support);
|
||||
ADDSYM(config_has_ffmpeg_support);
|
||||
ADDSYM(config_has_curl_support);
|
||||
ADDSYM(config_has_exceptions);
|
||||
|
||||
ADDSYM(config_has_package);
|
||||
@ -188,6 +191,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
||||
ADDSYM(is_running);
|
||||
ADDSYM(force_timeout);
|
||||
|
||||
// symbol not present
|
||||
if (!lmp->config_has_exceptions) return NULL;
|
||||
|
||||
lmp->has_exceptions = lmp->config_has_exceptions();
|
||||
if (lmp->has_exceptions) {
|
||||
ADDSYM(has_error);
|
||||
|
||||
@ -144,11 +144,14 @@ struct _liblammpsplugin {
|
||||
int (*get_mpi_comm)(void *);
|
||||
|
||||
int (*extract_setting)(void *, const char *);
|
||||
int *(*extract_global_datatype)(void *, const char *);
|
||||
int (*extract_global_datatype)(void *, const char *);
|
||||
void *(*extract_global)(void *, const char *);
|
||||
void *(*map_atom)(void *, const void *);
|
||||
int (*extract_pair_dimension)(void *, const char *);
|
||||
void *(*extract_pair)(void *, const char *);
|
||||
int (*map_atom)(void *, const void *);
|
||||
|
||||
int *(*extract_atom_datatype)(void *, const char *);
|
||||
int (*extract_atom_datatype)(void *, const char *);
|
||||
int (*extract_atom_size)(void *, const char *, int);
|
||||
void *(*extract_atom)(void *, const char *);
|
||||
|
||||
void *(*extract_compute)(void *, const char *, int, int);
|
||||
@ -201,6 +204,7 @@ struct _liblammpsplugin {
|
||||
int (*config_has_png_support)();
|
||||
int (*config_has_jpeg_support)();
|
||||
int (*config_has_ffmpeg_support)();
|
||||
int (*config_has_curl_support)();
|
||||
int (*config_has_exceptions)();
|
||||
|
||||
int (*config_has_package)(const char *);
|
||||
|
||||
@ -5,9 +5,9 @@ dimension 3
|
||||
atom_style full
|
||||
processors * * 1
|
||||
|
||||
pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long"
|
||||
pair_style lj/spica/coul/long 15.0
|
||||
bond_style harmonic
|
||||
angle_style sdk # compatible with "spica"
|
||||
angle_style spica
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
read_data data.sds.gz
|
||||
|
||||
@ -1,629 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
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
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
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
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 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
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
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/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5817 | 1.5817 | 1.5817 | 0.0 | 72.79
|
||||
Bond | 0.0031469 | 0.0031469 | 0.0031469 | 0.0 | 0.14
|
||||
Kspace | 0.17366 | 0.17366 | 0.17366 | 0.0 | 7.99
|
||||
Neigh | 0.37354 | 0.37354 | 0.37354 | 0.0 | 17.19
|
||||
Comm | 0.013652 | 0.013652 | 0.013652 | 0.0 | 0.63
|
||||
Output | 0.00026059 | 0.00026059 | 0.00026059 | 0.0 | 0.01
|
||||
Modify | 0.025484 | 0.025484 | 0.025484 | 0.0 | 1.17
|
||||
Other | | 0.001615 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
||||
140 253.85111 -5452.1838 -6473.4522 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4727 -6541.7817 1051.3091 -6646.6076 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4424 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3253 -6550.1124 999.78705 -6661.4235 26.200127 3.4336038
|
||||
190 250.80862 -5555.2554 -6564.2836 1009.0282 -6666.164 25.53634 3.3494288
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5975 | 1.5975 | 1.5975 | 0.0 | 78.58
|
||||
Bond | 0.0033164 | 0.0033164 | 0.0033164 | 0.0 | 0.16
|
||||
Kspace | 0.17349 | 0.17349 | 0.17349 | 0.0 | 8.53
|
||||
Neigh | 0.21971 | 0.21971 | 0.21971 | 0.0 | 10.81
|
||||
Comm | 0.012045 | 0.012045 | 0.012045 | 0.0 | 0.59
|
||||
Output | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.01
|
||||
Modify | 0.025034 | 0.025034 | 0.025034 | 0.0 | 1.23
|
||||
Other | | 0.001596 | | | 0.08
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11159 ave 11159 max 11159 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708083 ave 708083 max 708083 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.335
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
||||
colvars: Setting initial step number from LAMMPS: 200
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
||||
210 253.15303 -5538.5615 -6557.0215 1018.46 -6672.0498 37.67662 0.61219496
|
||||
220 245.19621 -5522.519 -6508.9679 986.44888 -6628.1899 36.657688 0.04864338
|
||||
230 258.69884 -5495.7275 -6536.4988 1040.7713 -6658.2885 34.857911 0.22092547
|
||||
240 260.79635 -5469.8678 -6519.0776 1049.2098 -6624.1801 31.576951 3.7574816
|
||||
250 269.07527 -5438.3946 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600014
|
||||
260 266.01049 -5397.3485 -6467.5353 1070.1868 -6580.2897 26.871917 8.3323097
|
||||
270 272.81313 -5350.882 -6448.4365 1097.5545 -6563.8231 23.114195 10.973131
|
||||
280 279.42263 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644027 8.5490492
|
||||
290 286.85172 -5260.841 -6414.8741 1154.0331 -6515.6798 28.574838 5.9100133
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79792e-05
|
||||
6 0.997005 1.02512e-05
|
||||
8 1.08 1.85102e-05
|
||||
10 1.111 9.98839e-06
|
||||
12 1.08 8.84111e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.8445e-05
|
||||
31 104.52 0.00168383
|
||||
300 291.52798 -5216.288 -6389.1341 1172.8462 -6503.1276 27.889154 2.2482459
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6047 | 1.6047 | 1.6047 | 0.0 | 77.46
|
||||
Bond | 0.0031033 | 0.0031033 | 0.0031033 | 0.0 | 0.15
|
||||
Kspace | 0.17325 | 0.17325 | 0.17325 | 0.0 | 8.36
|
||||
Neigh | 0.25117 | 0.25117 | 0.25117 | 0.0 | 12.12
|
||||
Comm | 0.012173 | 0.012173 | 0.012173 | 0.0 | 0.59
|
||||
Output | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
|
||||
Modify | 0.025317 | 0.025317 | 0.025317 | 0.0 | 1.22
|
||||
Other | | 0.001731 | | | 0.08
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11296 ave 11296 max 11296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708152 ave 708152 max 708152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.369
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -1,629 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
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
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
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
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 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
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
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/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40413 | 0.41468 | 0.42573 | 1.4 | 67.52
|
||||
Bond | 0.00056815 | 0.0011595 | 0.0017791 | 1.6 | 0.19
|
||||
Kspace | 0.056367 | 0.066512 | 0.076213 | 3.3 | 10.83
|
||||
Neigh | 0.095025 | 0.09507 | 0.095124 | 0.0 | 15.48
|
||||
Comm | 0.015385 | 0.015831 | 0.01623 | 0.2 | 2.58
|
||||
Output | 0.00026512 | 0.00034493 | 0.00057554 | 0.0 | 0.06
|
||||
Modify | 0.01938 | 0.019431 | 0.019474 | 0.0 | 3.16
|
||||
Other | | 0.001141 | | | 0.19
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
||||
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0941 -6559.6493 1019.5552 -6656.6677 23.293812 10.290217
|
||||
180 248.51161 -5550.3253 -6550.1124 999.78704 -6661.4235 26.200127 3.4336037
|
||||
190 250.80862 -5555.2553 -6564.2834 1009.0282 -6666.1638 25.53634 3.3494287
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40512 | 0.41306 | 0.42363 | 1.3 | 72.50
|
||||
Bond | 0.00061107 | 0.001151 | 0.0017512 | 1.4 | 0.20
|
||||
Kspace | 0.054393 | 0.063988 | 0.07198 | 3.0 | 11.23
|
||||
Neigh | 0.056063 | 0.056079 | 0.05609 | 0.0 | 9.84
|
||||
Comm | 0.013584 | 0.014145 | 0.014649 | 0.3 | 2.48
|
||||
Output | 0.00026965 | 0.00042897 | 0.00090265 | 0.0 | 0.08
|
||||
Modify | 0.019253 | 0.019257 | 0.01926 | 0.0 | 3.38
|
||||
Other | | 0.001623 | | | 0.28
|
||||
|
||||
Nlocal: 501 ave 513 max 481 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 6556.5 ave 6608 max 6514 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 177021 ave 182259 max 172089 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.335
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
||||
colvars: Setting initial step number from LAMMPS: 200
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
||||
210 253.15304 -5538.5615 -6557.0215 1018.46 -6672.0498 37.676621 0.61219486
|
||||
220 245.19621 -5522.5189 -6508.9678 986.44888 -6628.1898 36.657688 0.048643368
|
||||
230 258.69885 -5495.7276 -6536.4989 1040.7713 -6658.2887 34.857911 0.22092541
|
||||
240 260.79635 -5469.8677 -6519.0775 1049.2098 -6624.18 31.576952 3.7574818
|
||||
250 269.07527 -5438.3947 -6520.9115 1082.5167 -6616.4384 25.447674 8.6600013
|
||||
260 266.0105 -5397.3486 -6467.5354 1070.1868 -6580.2898 26.871917 8.3323096
|
||||
270 272.81314 -5350.8819 -6448.4364 1097.5545 -6563.823 23.114195 10.973131
|
||||
280 279.42263 -5307.9799 -6432.125 1124.1452 -6557.3367 33.644027 8.5490488
|
||||
290 286.8517 -5260.8409 -6414.874 1154.0331 -6515.6797 28.574839 5.9100135
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79792e-05
|
||||
6 0.997005 1.02512e-05
|
||||
8 1.08 1.85102e-05
|
||||
10 1.111 9.98838e-06
|
||||
12 1.08 8.84113e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.8445e-05
|
||||
31 104.52 0.00168382
|
||||
300 291.52794 -5216.2881 -6389.1342 1172.846 -6503.1276 27.889153 2.248246
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41044 | 0.41882 | 0.42773 | 1.1 | 71.60
|
||||
Bond | 0.00056911 | 0.0011486 | 0.0018017 | 1.4 | 0.20
|
||||
Kspace | 0.056211 | 0.064277 | 0.072168 | 2.7 | 10.99
|
||||
Neigh | 0.064606 | 0.064613 | 0.064617 | 0.0 | 11.05
|
||||
Comm | 0.013311 | 0.013966 | 0.015175 | 0.6 | 2.39
|
||||
Output | 0.00027871 | 0.00051689 | 0.0012221 | 0.0 | 0.09
|
||||
Modify | 0.019776 | 0.0199 | 0.020015 | 0.1 | 3.40
|
||||
Other | | 0.001705 | | | 0.29
|
||||
|
||||
Nlocal: 501 ave 513 max 472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 6612.75 ave 6681 max 6561 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 177038 ave 180136 max 170218 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.369
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,260 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
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
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
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
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 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
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
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/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars2":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46
|
||||
Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14
|
||||
Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72
|
||||
Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90
|
||||
Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62
|
||||
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01
|
||||
Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08
|
||||
Other | | 0.001465 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:02
|
||||
@ -1,260 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
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
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
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
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 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
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
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/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars2":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.629325 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 27.458 ns/day, 0.874 hours/ns, 158.900 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.4012 | 0.41532 | 0.42829 | 1.9 | 65.99
|
||||
Bond | 0.0005219 | 0.0011545 | 0.0018291 | 1.8 | 0.18
|
||||
Kspace | 0.059271 | 0.071301 | 0.084393 | 4.4 | 11.33
|
||||
Neigh | 0.10416 | 0.10419 | 0.10424 | 0.0 | 16.56
|
||||
Comm | 0.015643 | 0.016628 | 0.017256 | 0.5 | 2.64
|
||||
Output | 0.00025177 | 0.00033599 | 0.00058722 | 0.0 | 0.05
|
||||
Modify | 0.01912 | 0.019129 | 0.019141 | 0.0 | 3.04
|
||||
Other | | 0.001264 | | | 0.20
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,163 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
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
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
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
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 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
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
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/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 2.21146 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.814 ns/day, 3.071 hours/ns, 45.219 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 | 1.6195 | 1.6195 | 1.6195 | 0.0 | 73.23
|
||||
Bond | 0.0033534 | 0.0033534 | 0.0033534 | 0.0 | 0.15
|
||||
Kspace | 0.17464 | 0.17464 | 0.17464 | 0.0 | 7.90
|
||||
Neigh | 0.37337 | 0.37337 | 0.37337 | 0.0 | 16.88
|
||||
Comm | 0.013891 | 0.013891 | 0.013891 | 0.0 | 0.63
|
||||
Output | 0.00037336 | 0.00037336 | 0.00037336 | 0.0 | 0.02
|
||||
Modify | 0.024753 | 0.024753 | 0.024753 | 0.0 | 1.12
|
||||
Other | | 0.001613 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:02
|
||||
@ -1,163 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
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
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
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
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 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
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
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/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.620672 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 27.841 ns/day, 0.862 hours/ns, 161.116 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.4029 | 0.41752 | 0.4307 | 1.7 | 67.27
|
||||
Bond | 0.00054789 | 0.0011698 | 0.0018225 | 1.8 | 0.19
|
||||
Kspace | 0.055853 | 0.069798 | 0.083975 | 4.3 | 11.25
|
||||
Neigh | 0.096553 | 0.096622 | 0.096707 | 0.0 | 15.57
|
||||
Comm | 0.015383 | 0.016022 | 0.01632 | 0.3 | 2.58
|
||||
Output | 0.00033116 | 0.00057495 | 0.0012989 | 0.0 | 0.09
|
||||
Modify | 0.017549 | 0.017693 | 0.017826 | 0.1 | 2.85
|
||||
Other | | 0.001274 | | | 0.21
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
@ -1,158 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
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
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
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
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 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
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
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/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 2.2037 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.841 ns/day, 3.061 hours/ns, 45.378 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 | 1.5852 | 1.5852 | 1.5852 | 0.0 | 71.93
|
||||
Bond | 0.0032725 | 0.0032725 | 0.0032725 | 0.0 | 0.15
|
||||
Kspace | 0.17308 | 0.17308 | 0.17308 | 0.0 | 7.85
|
||||
Neigh | 0.4027 | 0.4027 | 0.4027 | 0.0 | 18.27
|
||||
Comm | 0.014041 | 0.014041 | 0.014041 | 0.0 | 0.64
|
||||
Output | 0.00032306 | 0.00032306 | 0.00032306 | 0.0 | 0.01
|
||||
Modify | 0.023546 | 0.023546 | 0.023546 | 0.0 | 1.07
|
||||
Other | | 0.001546 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:02
|
||||
@ -1,158 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
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
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
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
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 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
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
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/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40372 | 0.41244 | 0.41714 | 0.8 | 66.95
|
||||
Bond | 0.00053573 | 0.0011384 | 0.0017946 | 1.8 | 0.18
|
||||
Kspace | 0.060087 | 0.063993 | 0.07306 | 2.1 | 10.39
|
||||
Neigh | 0.1033 | 0.10349 | 0.1036 | 0.0 | 16.80
|
||||
Comm | 0.01568 | 0.016453 | 0.017178 | 0.5 | 2.67
|
||||
Output | 0.00028253 | 0.00032026 | 0.00043178 | 0.0 | 0.05
|
||||
Modify | 0.016238 | 0.016955 | 0.017704 | 0.5 | 2.75
|
||||
Other | | 0.001239 | | | 0.20
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1
Normal file
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1
Normal file
@ -0,0 +1,732 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
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
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
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 = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
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
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
The final output state file will be "out.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
|
||||
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 7
|
||||
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) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.897199 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.260 ns/day, 1.246 hours/ns, 111.458 timesteps/s, 223.362 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71298 | 0.71298 | 0.71298 | 0.0 | 79.47
|
||||
Bond | 0.001284 | 0.001284 | 0.001284 | 0.0 | 0.14
|
||||
Kspace | 0.041232 | 0.041232 | 0.041232 | 0.0 | 4.60
|
||||
Neigh | 0.1277 | 0.1277 | 0.1277 | 0.0 | 14.23
|
||||
Comm | 0.0033285 | 0.0033285 | 0.0033285 | 0.0 | 0.37
|
||||
Output | 0.00017467 | 0.00017467 | 0.00017467 | 0.0 | 0.02
|
||||
Modify | 0.010003 | 0.010003 | 0.010003 | 0.0 | 1.11
|
||||
Other | | 0.0004941 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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
|
||||
Current simulation parameters: initial step = 100, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
|
||||
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1372 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4236 26.200127 3.4336037
|
||||
190 250.80862 -5555.2554 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.855092 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 20.208 ns/day, 1.188 hours/ns, 116.946 timesteps/s, 234.361 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71954 | 0.71954 | 0.71954 | 0.0 | 84.15
|
||||
Bond | 0.0012655 | 0.0012655 | 0.0012655 | 0.0 | 0.15
|
||||
Kspace | 0.042826 | 0.042826 | 0.042826 | 0.0 | 5.01
|
||||
Neigh | 0.078128 | 0.078128 | 0.078128 | 0.0 | 9.14
|
||||
Comm | 0.0029003 | 0.0029003 | 0.0029003 | 0.0 | 0.34
|
||||
Output | 0.00016605 | 0.00016605 | 0.00016605 | 0.0 | 0.02
|
||||
Modify | 0.0097753 | 0.0097753 | 0.0097753 | 0.0 | 1.14
|
||||
Other | | 0.0004882 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11159 ave 11159 max 11159 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708083 ave 708083 max 708083 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.33483
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
Setting initial step number from MD engine: 200
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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
|
||||
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 200, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
----------------------------------------------------------------------
|
||||
Loading state from text file "out.colvars.state".
|
||||
Restarting collective variable "one" from value: 10.0128
|
||||
Restarting collective variable "two" from value: 9.62236
|
||||
Restarted harmonic bias "h_pot" with step number 200.
|
||||
----------------------------------------------------------------------
|
||||
The final output state file will be "out2.colvars.state".
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
|
||||
210 253.15302 -5538.5614 -6557.0213 1018.4599 -6672.0496 37.676621 0.61219488
|
||||
220 245.19621 -5522.5192 -6508.9681 986.44887 -6628.19 36.657688 0.048643387
|
||||
230 258.69885 -5495.7277 -6536.499 1040.7713 -6658.2888 34.857911 0.2209256
|
||||
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.1799 31.576952 3.7574815
|
||||
250 269.07527 -5438.3947 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600023
|
||||
260 266.01046 -5397.3484 -6467.5351 1070.1867 -6580.2895 26.871919 8.3323102
|
||||
270 272.81307 -5350.882 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
|
||||
280 279.42264 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644021 8.5490492
|
||||
290 286.85168 -5260.8411 -6414.874 1154.033 -6515.6797 28.574838 5.9100104
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.111 1.79793e-05 9
|
||||
Bond: 6 0.997005 1.02512e-05 6
|
||||
Bond: 8 1.08 1.85103e-05 7
|
||||
Bond: 10 1.111 9.9884e-06 8
|
||||
Bond: 12 1.08 8.84114e-06 9
|
||||
Bond: 14 0.960008 0 1
|
||||
Bond: 18 0.957203 1.8445e-05 1280
|
||||
Angle: 31 104.52 0.00168383 640
|
||||
300 291.52794 -5216.288 -6389.1341 1172.846 -6503.1276 27.889149 2.2482427
|
||||
Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.86889 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.887 ns/day, 1.207 hours/ns, 115.089 timesteps/s, 230.639 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.72728 | 0.72728 | 0.72728 | 0.0 | 83.70
|
||||
Bond | 0.0012755 | 0.0012755 | 0.0012755 | 0.0 | 0.15
|
||||
Kspace | 0.041631 | 0.041631 | 0.041631 | 0.0 | 4.79
|
||||
Neigh | 0.085283 | 0.085283 | 0.085283 | 0.0 | 9.82
|
||||
Comm | 0.0029986 | 0.0029986 | 0.0029986 | 0.0 | 0.35
|
||||
Output | 0.00013272 | 0.00013272 | 0.00013272 | 0.0 | 0.02
|
||||
Modify | 0.0097972 | 0.0097972 | 0.0097972 | 0.0 | 1.13
|
||||
Other | | 0.0004882 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11296 ave 11296 max 11296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708152 ave 708152 max 708152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.36926
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:02
|
||||
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4
Normal file
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4
Normal file
@ -0,0 +1,732 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
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
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
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 = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
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
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
The final output state file will be "out.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
|
||||
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 7
|
||||
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) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.246405 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 70.128 ns/day, 0.342 hours/ns, 405.836 timesteps/s, 813.295 katom-step/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 | 0.17765 | 0.18092 | 0.18373 | 0.6 | 73.42
|
||||
Bond | 0.00021581 | 0.00045219 | 0.00069916 | 0.0 | 0.18
|
||||
Kspace | 0.018035 | 0.020459 | 0.023812 | 1.7 | 8.30
|
||||
Neigh | 0.032165 | 0.032193 | 0.032207 | 0.0 | 13.07
|
||||
Comm | 0.00566 | 0.0058533 | 0.0060088 | 0.2 | 2.38
|
||||
Output | 0.00012205 | 0.00014069 | 0.00019404 | 0.0 | 0.06
|
||||
Modify | 0.0059979 | 0.0060225 | 0.0060368 | 0.0 | 2.44
|
||||
Other | | 0.0003631 | | | 0.15
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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
|
||||
Current simulation parameters: initial step = 100, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
|
||||
140 253.85111 -5452.1837 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7816 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4235 26.200127 3.4336036
|
||||
190 250.80862 -5555.2555 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.238087 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 72.578 ns/day, 0.331 hours/ns, 420.014 timesteps/s, 841.709 katom-step/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17913 | 0.18408 | 0.19082 | 1.1 | 77.32
|
||||
Bond | 0.00019617 | 0.00044139 | 0.00071286 | 0.0 | 0.19
|
||||
Kspace | 0.016186 | 0.022449 | 0.02737 | 3.0 | 9.43
|
||||
Neigh | 0.018728 | 0.018753 | 0.018777 | 0.0 | 7.88
|
||||
Comm | 0.0052171 | 0.0055397 | 0.0058422 | 0.3 | 2.33
|
||||
Output | 0.00012326 | 0.00014453 | 0.00020506 | 0.0 | 0.06
|
||||
Modify | 0.0062505 | 0.0062725 | 0.0062944 | 0.0 | 2.63
|
||||
Other | | 0.0004069 | | | 0.17
|
||||
|
||||
Nlocal: 501 ave 513 max 481 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 6556.5 ave 6608 max 6514 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 177021 ave 182259 max 172089 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.33483
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
Setting initial step number from MD engine: 200
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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
|
||||
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 200, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
----------------------------------------------------------------------
|
||||
Loading state from text file "out.colvars.state".
|
||||
Restarting collective variable "one" from value: 10.0128
|
||||
Restarting collective variable "two" from value: 9.62236
|
||||
Restarted harmonic bias "h_pot" with step number 200.
|
||||
----------------------------------------------------------------------
|
||||
The final output state file will be "out2.colvars.state".
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
|
||||
210 253.15302 -5538.5615 -6557.0215 1018.4599 -6672.0498 37.676621 0.61219488
|
||||
220 245.19621 -5522.5191 -6508.9679 986.44887 -6628.1899 36.657688 0.048643387
|
||||
230 258.69885 -5495.7275 -6536.4989 1040.7713 -6658.2886 34.857911 0.22092559
|
||||
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.18 31.576952 3.7574815
|
||||
250 269.07527 -5438.3946 -6520.9113 1082.5167 -6616.4382 25.447675 8.6600023
|
||||
260 266.01046 -5397.3485 -6467.5352 1070.1867 -6580.2896 26.871919 8.3323104
|
||||
270 272.81307 -5350.8819 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
|
||||
280 279.42265 -5307.9799 -6432.1251 1124.1452 -6557.3368 33.644022 8.5490489
|
||||
290 286.85168 -5260.841 -6414.874 1154.033 -6515.6797 28.574838 5.9100102
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.111 1.79793e-05 9
|
||||
Bond: 6 0.997005 1.02512e-05 6
|
||||
Bond: 8 1.08 1.85103e-05 7
|
||||
Bond: 10 1.111 9.9884e-06 8
|
||||
Bond: 12 1.08 8.84114e-06 9
|
||||
Bond: 14 0.960008 0 1
|
||||
Bond: 18 0.957203 1.8445e-05 1280
|
||||
Angle: 31 104.52 0.00168383 640
|
||||
300 291.52793 -5216.288 -6389.1341 1172.846 -6503.1275 27.88915 2.2482428
|
||||
Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.245933 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 70.263 ns/day, 0.342 hours/ns, 406.614 timesteps/s, 814.854 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17862 | 0.18666 | 0.19126 | 1.2 | 75.90
|
||||
Bond | 0.00021974 | 0.00048505 | 0.00077708 | 0.0 | 0.20
|
||||
Kspace | 0.018338 | 0.02317 | 0.031148 | 3.4 | 9.42
|
||||
Neigh | 0.022128 | 0.022183 | 0.022222 | 0.0 | 9.02
|
||||
Comm | 0.0059137 | 0.0060593 | 0.0064247 | 0.3 | 2.46
|
||||
Output | 0.00014648 | 0.00015946 | 0.00019596 | 0.0 | 0.06
|
||||
Modify | 0.0067012 | 0.00674 | 0.0067814 | 0.0 | 2.74
|
||||
Other | | 0.0004738 | | | 0.19
|
||||
|
||||
Nlocal: 501 ave 513 max 472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 6612.75 ave 6681 max 6561 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 177038 ave 180136 max 170218 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.36926
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1
Normal file
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1
Normal file
@ -0,0 +1,344 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
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
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
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 = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
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
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars2":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 4 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10 }
|
||||
# targetCenters = { 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
The final output state file will be "peptide2.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
|
||||
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 7
|
||||
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) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.907882 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.033 ns/day, 1.261 hours/ns, 110.146 timesteps/s, 220.734 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71563 | 0.71563 | 0.71563 | 0.0 | 78.82
|
||||
Bond | 0.0013267 | 0.0013267 | 0.0013267 | 0.0 | 0.15
|
||||
Kspace | 0.042157 | 0.042157 | 0.042157 | 0.0 | 4.64
|
||||
Neigh | 0.13452 | 0.13452 | 0.13452 | 0.0 | 14.82
|
||||
Comm | 0.0034995 | 0.0034995 | 0.0034995 | 0.0 | 0.39
|
||||
Output | 0.00014584 | 0.00014584 | 0.00014584 | 0.0 | 0.02
|
||||
Modify | 0.010115 | 0.010115 | 0.010115 | 0.0 | 1.11
|
||||
Other | | 0.0004888 | | | 0.05
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Total wall time: 0:00:00
|
||||
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4
Normal file
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4
Normal file
@ -0,0 +1,344 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
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
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
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 = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
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
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars2":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 4 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10 }
|
||||
# targetCenters = { 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
The final output state file will be "peptide2.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
|
||||
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 7
|
||||
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) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.253421 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 68.187 ns/day, 0.352 hours/ns, 394.600 timesteps/s, 790.779 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1771 | 0.18185 | 0.18625 | 0.8 | 71.76
|
||||
Bond | 0.00028771 | 0.00056007 | 0.00087366 | 0.0 | 0.22
|
||||
Kspace | 0.017434 | 0.021451 | 0.026345 | 2.4 | 8.46
|
||||
Neigh | 0.035481 | 0.035495 | 0.035512 | 0.0 | 14.01
|
||||
Comm | 0.0064003 | 0.0065098 | 0.0065994 | 0.1 | 2.57
|
||||
Output | 0.00012417 | 0.00013888 | 0.00018109 | 0.0 | 0.05
|
||||
Modify | 0.0069389 | 0.0069521 | 0.0069617 | 0.0 | 2.74
|
||||
Other | | 0.0004667 | | | 0.18
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Total wall time: 0:00:00
|
||||
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1
Normal file
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1
Normal file
@ -0,0 +1,194 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
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
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
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 = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
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
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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 7
|
||||
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) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.893963 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.330 ns/day, 1.242 hours/ns, 111.861 timesteps/s, 224.170 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.7114 | 0.7114 | 0.7114 | 0.0 | 79.58
|
||||
Bond | 0.0012663 | 0.0012663 | 0.0012663 | 0.0 | 0.14
|
||||
Kspace | 0.041962 | 0.041962 | 0.041962 | 0.0 | 4.69
|
||||
Neigh | 0.12542 | 0.12542 | 0.12542 | 0.0 | 14.03
|
||||
Comm | 0.0033466 | 0.0033466 | 0.0033466 | 0.0 | 0.37
|
||||
Output | 0.00017765 | 0.00017765 | 0.00017765 | 0.0 | 0.02
|
||||
Modify | 0.0098927 | 0.0098927 | 0.0098927 | 0.0 | 1.11
|
||||
Other | | 0.0005014 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4
Normal file
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4
Normal file
@ -0,0 +1,194 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
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
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
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 = 0.010 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
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
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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 7
|
||||
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) = 16.01 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.247541 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 69.806 ns/day, 0.344 hours/ns, 403.973 timesteps/s, 809.561 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17778 | 0.18129 | 0.18529 | 0.8 | 73.24
|
||||
Bond | 0.00024025 | 0.00049912 | 0.00080235 | 0.0 | 0.20
|
||||
Kspace | 0.016204 | 0.0204 | 0.023648 | 2.3 | 8.24
|
||||
Neigh | 0.032425 | 0.032462 | 0.032496 | 0.0 | 13.11
|
||||
Comm | 0.0063955 | 0.0065509 | 0.0067449 | 0.2 | 2.65
|
||||
Output | 0.0001675 | 0.00018071 | 0.00021385 | 0.0 | 0.07
|
||||
Modify | 0.0057027 | 0.0057304 | 0.0057568 | 0.0 | 2.31
|
||||
Other | | 0.0004289 | | | 0.17
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1
Normal file
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1
Normal file
@ -0,0 +1,189 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
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
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
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 = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
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
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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 7
|
||||
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) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.910778 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 18.973 ns/day, 1.265 hours/ns, 109.796 timesteps/s, 220.032 katom-step/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71746 | 0.71746 | 0.71746 | 0.0 | 78.77
|
||||
Bond | 0.0012756 | 0.0012756 | 0.0012756 | 0.0 | 0.14
|
||||
Kspace | 0.042462 | 0.042462 | 0.042462 | 0.0 | 4.66
|
||||
Neigh | 0.13497 | 0.13497 | 0.13497 | 0.0 | 14.82
|
||||
Comm | 0.0036247 | 0.0036247 | 0.0036247 | 0.0 | 0.40
|
||||
Output | 0.00016145 | 0.00016145 | 0.00016145 | 0.0 | 0.02
|
||||
Modify | 0.010258 | 0.010258 | 0.010258 | 0.0 | 1.13
|
||||
Other | | 0.0005695 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4
Normal file
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4
Normal file
@ -0,0 +1,189 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
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
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
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 = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
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
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
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 7
|
||||
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) = 16.01 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.248812 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 69.450 ns/day, 0.346 hours/ns, 401.910 timesteps/s, 805.428 katom-step/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 | 0.17522 | 0.18002 | 0.18454 | 1.0 | 72.35
|
||||
Bond | 0.00020312 | 0.00044793 | 0.00074786 | 0.0 | 0.18
|
||||
Kspace | 0.016556 | 0.021002 | 0.026079 | 3.0 | 8.44
|
||||
Neigh | 0.035695 | 0.03571 | 0.03572 | 0.0 | 14.35
|
||||
Comm | 0.0057324 | 0.0058127 | 0.005874 | 0.1 | 2.34
|
||||
Output | 0.00013005 | 0.00013946 | 0.00016548 | 0.0 | 0.06
|
||||
Modify | 0.00526 | 0.0052645 | 0.005272 | 0.0 | 2.12
|
||||
Other | | 0.0004197 | | | 0.17
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
@ -1,17 +1,17 @@
|
||||
configuration {
|
||||
step 200
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00127732034965e+01
|
||||
x 10.012773203962
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.62235997490241e+00
|
||||
x 9.6223599748448
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
configuration {
|
||||
step 100
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00136989326255e+01
|
||||
x 10.013698932648
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 1.00648830006091e+01
|
||||
x 10.064883000604
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -13,191 +13,191 @@
|
||||
11 1.01744058364969e+01 8.66916428851601e+00
|
||||
12 1.01894584969823e+01 8.75011341291751e+00
|
||||
13 1.02015949657517e+01 8.81261373358815e+00
|
||||
14 1.02107634786499e+01 8.86010572643564e+00
|
||||
14 1.02107634786498e+01 8.86010572643564e+00
|
||||
15 1.02172802335367e+01 8.89996164389908e+00
|
||||
16 1.02217586687617e+01 8.94046117354318e+00
|
||||
17 1.02249400729821e+01 8.98764357480963e+00
|
||||
18 1.02274821194763e+01 9.04385418276306e+00
|
||||
19 1.02297694921722e+01 9.10767828090644e+00
|
||||
20 1.02317948794015e+01 9.17521818721732e+00
|
||||
20 1.02317948794015e+01 9.17521818721733e+00
|
||||
21 1.02331324174422e+01 9.24256921345538e+00
|
||||
22 1.02330115052436e+01 9.30670040650459e+00
|
||||
22 1.02330115052436e+01 9.30670040650458e+00
|
||||
23 1.02304888847637e+01 9.36477739916766e+00
|
||||
24 1.02246905091409e+01 9.41471338314027e+00
|
||||
25 1.02150557312054e+01 9.45578119421866e+00
|
||||
26 1.02015018849614e+01 9.48855148434622e+00
|
||||
27 1.01844563445019e+01 9.51414398880334e+00
|
||||
26 1.02015018849613e+01 9.48855148434622e+00
|
||||
27 1.01844563445019e+01 9.51414398880333e+00
|
||||
28 1.01647618536435e+01 9.53348342780342e+00
|
||||
29 1.01435075836914e+01 9.54736918677922e+00
|
||||
30 1.01218448127414e+01 9.55679294480281e+00
|
||||
30 1.01218448127414e+01 9.55679294480282e+00
|
||||
31 1.01008234685872e+01 9.56289707955055e+00
|
||||
32 1.00812605992407e+01 9.56689852729787e+00
|
||||
33 1.00636482078211e+01 9.57008522470066e+00
|
||||
34 1.00481219532447e+01 9.57404682801174e+00
|
||||
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131 1.01518709223691e+01 9.98617497219244e+00
|
||||
132 1.01475657134909e+01 9.99754506714391e+00
|
||||
133 1.01411666159632e+01 1.00106710660677e+01
|
||||
134 1.01332318744629e+01 1.00230220360430e+01
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
145 1.00223855041248e+01 9.81818968320503e+00
|
||||
146 1.00118066120332e+01 9.77759398937178e+00
|
||||
147 1.00015635424482e+01 9.73590632987673e+00
|
||||
148 9.99195808450856e+00 9.69551862651774e+00
|
||||
149 9.98332973840472e+00 9.65911623099469e+00
|
||||
150 9.97599905822999e+00 9.62915505892649e+00
|
||||
151 9.97019367845638e+00 9.60716909703526e+00
|
||||
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|
||||
153 9.96324606044969e+00 9.58559881066392e+00
|
||||
154 9.96169276237047e+00 9.58153758575953e+00
|
||||
155 9.96092625152242e+00 9.57763829328116e+00
|
||||
156 9.96054315740228e+00 9.57093750810941e+00
|
||||
157 9.96023482376251e+00 9.55965895382487e+00
|
||||
158 9.95985352333786e+00 9.54367776304373e+00
|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
200 1.00127732039621e+01 9.62235997484479e+00
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
configuration {
|
||||
step 300
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 9.95315918568411e+00
|
||||
x 9.9531592295885
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.79318883680258e+00
|
||||
x 9.7931889789213
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -1,102 +1,102 @@
|
||||
# step one two
|
||||
200 1.00127732034965e+01 9.62235997490241e+00
|
||||
201 1.00139198864982e+01 9.61766167925624e+00
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
293 1.00255913568518e+01 9.69130440474672e+00
|
||||
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|
||||
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|
||||
296 9.99406221883501e+00 9.74140402524052e+00
|
||||
297 9.98250803362175e+00 9.75776438941627e+00
|
||||
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|
||||
299 9.96175637151037e+00 9.78379375044905e+00
|
||||
300 9.95315918568411e+00 9.79318883680258e+00
|
||||
200 1.00127732039621e+01 9.62235997484479e+00
|
||||
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|
||||
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|
||||
203 1.00172741984288e+01 9.63964899413135e+00
|
||||
204 1.00189052034286e+01 9.66786718668113e+00
|
||||
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|
||||
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|
||||
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|
||||
208 1.00162005542527e+01 9.83091553193592e+00
|
||||
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|
||||
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|
||||
211 1.00009200570685e+01 9.90798080630807e+00
|
||||
212 9.99531475670037e+00 9.92127385350745e+00
|
||||
213 9.99063399978946e+00 9.93157198491364e+00
|
||||
214 9.98737188290188e+00 9.94051482558046e+00
|
||||
215 9.98567126870035e+00 9.94885527853167e+00
|
||||
216 9.98528703143402e+00 9.95646746044078e+00
|
||||
217 9.98565831825084e+00 9.96275739920543e+00
|
||||
218 9.98606722850532e+00 9.96730423316541e+00
|
||||
219 9.98583581006681e+00 9.97036378874527e+00
|
||||
220 9.98450999905139e+00 9.97292736402649e+00
|
||||
221 9.98198432974296e+00 9.97627440161597e+00
|
||||
222 9.97853676608100e+00 9.98127101043889e+00
|
||||
223 9.97475981847134e+00 9.98785371579891e+00
|
||||
224 9.97140283904510e+00 9.99492286559338e+00
|
||||
225 9.96917134637541e+00 1.00005443234936e+01
|
||||
226 9.96854520536988e+00 1.00023222900809e+01
|
||||
227 9.96967372102824e+00 9.99790272698630e+00
|
||||
228 9.97237632329275e+00 9.98555959429830e+00
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
239 1.00373944894039e+01 9.73349214878674e+00
|
||||
240 1.00463193546284e+01 9.72980720512224e+00
|
||||
241 1.00548769529672e+01 9.72611598750665e+00
|
||||
242 1.00626420263492e+01 9.72152571786963e+00
|
||||
243 1.00693108979996e+01 9.71531422666390e+00
|
||||
244 1.00747299927796e+01 9.70668631833486e+00
|
||||
245 1.00788810840328e+01 9.69472081315003e+00
|
||||
246 1.00818281015229e+01 9.67872528846535e+00
|
||||
247 1.00836382438846e+01 9.65899114629446e+00
|
||||
248 1.00843077202414e+01 9.63702965268533e+00
|
||||
249 1.00837304312378e+01 9.61431309843794e+00
|
||||
250 1.00817369677632e+01 9.59193246490958e+00
|
||||
251 1.00781951275561e+01 9.57162231665577e+00
|
||||
252 1.00731274389447e+01 9.55557271498134e+00
|
||||
253 1.00667870699195e+01 9.54559998431332e+00
|
||||
254 1.00596599010604e+01 9.54253145213164e+00
|
||||
255 1.00523957143832e+01 9.54593690642836e+00
|
||||
256 1.00457028598538e+01 9.55423080384305e+00
|
||||
257 1.00402419064054e+01 9.56514760196478e+00
|
||||
258 1.00365398159221e+01 9.57641295373454e+00
|
||||
259 1.00349276804438e+01 9.58620622717253e+00
|
||||
260 1.00355020510841e+01 9.59332345585722e+00
|
||||
261 1.00381137733017e+01 9.59732187421620e+00
|
||||
262 1.00423906427137e+01 9.59837617102817e+00
|
||||
263 1.00477959872900e+01 9.59679323453788e+00
|
||||
264 1.00537068694862e+01 9.59269522224878e+00
|
||||
265 1.00594937939774e+01 9.58610119961332e+00
|
||||
266 1.00645871442695e+01 9.57722116190429e+00
|
||||
267 1.00685317208695e+01 9.56668493059359e+00
|
||||
268 1.00710358435525e+01 9.55556250017823e+00
|
||||
269 1.00720144628669e+01 9.54520977349603e+00
|
||||
270 1.00716145056864e+01 9.53703780013997e+00
|
||||
271 1.00701992741473e+01 9.53227488069496e+00
|
||||
272 1.00682809229059e+01 9.53173332532930e+00
|
||||
273 1.00663988579612e+01 9.53554942356440e+00
|
||||
274 1.00649733547668e+01 9.54299861430164e+00
|
||||
275 1.00641836945973e+01 9.55262143202964e+00
|
||||
276 1.00639179095174e+01 9.56271517715327e+00
|
||||
277 1.00638154316074e+01 9.57192148613520e+00
|
||||
278 1.00633854335686e+01 9.57957875400668e+00
|
||||
279 1.00621627016565e+01 9.58572327370357e+00
|
||||
280 1.00598571070638e+01 9.59085686592320e+00
|
||||
281 1.00564566229803e+01 9.59567423699651e+00
|
||||
282 1.00522576689401e+01 9.60085551333600e+00
|
||||
283 1.00478091881844e+01 9.60690041329352e+00
|
||||
284 1.00437767554115e+01 9.61396710318380e+00
|
||||
285 1.00407546608873e+01 9.62178121653831e+00
|
||||
286 1.00390772967935e+01 9.62975551670189e+00
|
||||
287 1.00386905666453e+01 9.63733600598964e+00
|
||||
288 1.00391292301728e+01 9.64435235461356e+00
|
||||
289 1.00396076684883e+01 9.65114132457984e+00
|
||||
290 1.00391967232973e+01 9.65843914091158e+00
|
||||
291 1.00370408787737e+01 9.66713746391752e+00
|
||||
292 1.00325613002434e+01 9.67798048381559e+00
|
||||
293 1.00255913122523e+01 9.69130455064462e+00
|
||||
294 1.00164043783898e+01 9.70689857240811e+00
|
||||
295 1.00056261042358e+01 9.72399828398139e+00
|
||||
296 9.99406220236070e+00 9.74140420689973e+00
|
||||
297 9.98250803047048e+00 9.75776457125789e+00
|
||||
298 9.97160203186903e+00 9.77203086770013e+00
|
||||
299 9.96175639897897e+00 9.78379391142304e+00
|
||||
300 9.95315922958854e+00 9.79318897892133e+00
|
||||
|
||||
@ -1,12 +1,12 @@
|
||||
configuration {
|
||||
step 100
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00387423506482e+01
|
||||
x 10.038742350674
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -20,16 +20,16 @@
|
||||
18 9.41602481112176e+00
|
||||
19 9.44413580740584e+00
|
||||
20 9.49001346044027e+00
|
||||
21 9.55036359015270e+00
|
||||
22 9.62258602486444e+00
|
||||
23 9.70460545744668e+00
|
||||
21 9.55036359015271e+00
|
||||
22 9.62258602486445e+00
|
||||
23 9.70460545744666e+00
|
||||
24 9.79475465622561e+00
|
||||
25 9.89135302429916e+00
|
||||
26 9.99213332770717e+00
|
||||
25 9.89135302429913e+00
|
||||
26 9.99213332770716e+00
|
||||
27 1.00938522423366e+01
|
||||
28 1.01925371414626e+01
|
||||
29 1.02845129002944e+01
|
||||
30 1.03676671987640e+01
|
||||
30 1.03676671987639e+01
|
||||
31 1.04416385355998e+01
|
||||
32 1.05071349561950e+01
|
||||
33 1.05650463398331e+01
|
||||
@ -41,39 +41,39 @@
|
||||
39 1.07331870068021e+01
|
||||
40 1.07158913924701e+01
|
||||
41 1.06789115566470e+01
|
||||
42 1.06198840652253e+01
|
||||
42 1.06198840652254e+01
|
||||
43 1.05380097743725e+01
|
||||
44 1.04346581978275e+01
|
||||
45 1.03132910149185e+01
|
||||
46 1.01792819503691e+01
|
||||
46 1.01792819503692e+01
|
||||
47 1.00398949454818e+01
|
||||
48 9.90373650268307e+00
|
||||
49 9.77934647164350e+00
|
||||
50 9.67343955381284e+00
|
||||
51 9.58957255517495e+00
|
||||
52 9.52771577288560e+00
|
||||
53 9.48463495848957e+00
|
||||
54 9.45495747488851e+00
|
||||
55 9.43277083061229e+00
|
||||
56 9.41329510571902e+00
|
||||
57 9.39417852043035e+00
|
||||
49 9.77934647164349e+00
|
||||
50 9.67343955381283e+00
|
||||
51 9.58957255517494e+00
|
||||
52 9.52771577288559e+00
|
||||
53 9.48463495848955e+00
|
||||
54 9.45495747488850e+00
|
||||
55 9.43277083061230e+00
|
||||
56 9.41329510571900e+00
|
||||
57 9.39417852043034e+00
|
||||
58 9.37607916767444e+00
|
||||
59 9.36243879601093e+00
|
||||
60 9.35853234890725e+00
|
||||
61 9.36993739187210e+00
|
||||
62 9.40084256925489e+00
|
||||
59 9.36243879601092e+00
|
||||
60 9.35853234890724e+00
|
||||
61 9.36993739187209e+00
|
||||
62 9.40084256925487e+00
|
||||
63 9.45286356660258e+00
|
||||
64 9.52464585631223e+00
|
||||
65 9.61230948096192e+00
|
||||
66 9.71074418990813e+00
|
||||
67 9.81507236552599e+00
|
||||
68 9.92117974657176e+00
|
||||
69 1.00244259961919e+01
|
||||
66 9.71074418990814e+00
|
||||
67 9.81507236552600e+00
|
||||
68 9.92117974657179e+00
|
||||
69 1.00244259961920e+01
|
||||
70 1.01178306268727e+01
|
||||
71 1.01986985644537e+01
|
||||
71 1.01986985644538e+01
|
||||
72 1.02671003889995e+01
|
||||
73 1.03213098011429e+01
|
||||
74 1.03597236984298e+01
|
||||
73 1.03213098011430e+01
|
||||
74 1.03597236984299e+01
|
||||
75 1.03817789163109e+01
|
||||
76 1.03880650963390e+01
|
||||
77 1.03809140245635e+01
|
||||
@ -82,21 +82,21 @@
|
||||
80 1.03243676495902e+01
|
||||
81 1.03082131278348e+01
|
||||
82 1.02961310659179e+01
|
||||
83 1.02862115513553e+01
|
||||
83 1.02862115513552e+01
|
||||
84 1.02756073299153e+01
|
||||
85 1.02618115461408e+01
|
||||
86 1.02435127550163e+01
|
||||
87 1.02212112849545e+01
|
||||
88 1.01972788307491e+01
|
||||
89 1.01743918261207e+01
|
||||
89 1.01743918261206e+01
|
||||
90 1.01538328424605e+01
|
||||
91 1.01363005552771e+01
|
||||
92 1.01223066231827e+01
|
||||
93 1.01118037967830e+01
|
||||
92 1.01223066231826e+01
|
||||
93 1.01118037967829e+01
|
||||
94 1.01038502876980e+01
|
||||
95 1.00967012947728e+01
|
||||
96 1.00885779123137e+01
|
||||
97 1.00784256309007e+01
|
||||
98 1.00661429612272e+01
|
||||
99 1.00524913461711e+01
|
||||
100 1.00387423506482e+01
|
||||
95 1.00967012947726e+01
|
||||
96 1.00885779123133e+01
|
||||
97 1.00784256308996e+01
|
||||
98 1.00661429612359e+01
|
||||
99 1.00524913461887e+01
|
||||
100 1.00387423506735e+01
|
||||
|
||||
@ -16,7 +16,7 @@ variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
|
||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} -0.5 0.5 units box
|
||||
create_box 4 box
|
||||
lattice sq $a
|
||||
|
||||
|
||||
@ -14,7 +14,7 @@ variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
|
||||
region box block -$L $L -$L $L 0 $a units box
|
||||
region box block -$L $L -$L $L -0.5 0.5 units box
|
||||
create_box 2 box
|
||||
lattice sq $a
|
||||
|
||||
|
||||
@ -1,40 +1,40 @@
|
||||
variable sname index ch4
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
#dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
# Dynamics
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
#dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
#dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
|
||||
run 100000
|
||||
run 100000
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
variable sname index ch4
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
@ -24,8 +24,8 @@ variable erres equal c_energies[4]
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres
|
||||
|
||||
min_style cg
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
minimize 0 1e-6 2000 4000
|
||||
#dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
minimize 0 1e-6 2000 4000
|
||||
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
variable sname index ch4_ionized
|
||||
variable sname index ch4_ionized
|
||||
|
||||
units electron
|
||||
newton on
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 5000.0 0 0
|
||||
pair_coeff * *
|
||||
pair_style eff/cut 5000.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
# minimize
|
||||
|
||||
@ -20,23 +20,23 @@ min_modify line quadratic
|
||||
minimize 0 1.0e-6 10000 100000
|
||||
|
||||
# dynamics
|
||||
compute effTemp all temp/eff
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# equilibrate
|
||||
timestep 0.001
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
timestep 0.001
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
|
||||
# the custom dump includes the radii
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
#dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
#dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
|
||||
run 1000000
|
||||
run 1000000
|
||||
|
||||
fix 2 all nve/eff
|
||||
fix 2 all nve/eff
|
||||
|
||||
run 1000000
|
||||
run 1000000
|
||||
|
||||
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.1
Normal file
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.1
Normal file
@ -0,0 +1,266 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.ch4
|
||||
Reading data file ...
|
||||
orthogonal box = (-500 -500 -500) to (500 500 500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
15 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 102
|
||||
ghost atom cutoff = 102
|
||||
binsize = 51, bins = 20 20 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.405 | 5.405 | 5.405 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -27.314082 0 -27.314082 -56588.53
|
||||
1000 0 -34.07448 0 -34.07448 1.3464499
|
||||
Loop time of 0.0308104 on 1 procs for 1000 steps with 15 atoms
|
||||
|
||||
88.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-27.3140820331247 -34.0744796893375 -34.0744796893447
|
||||
Force two-norm initial, final = 10.728716 0.00017815706
|
||||
Force max component initial, final = 6.1727999 8.2675815e-05
|
||||
Final line search alpha, max atom move = 1 8.2675815e-05
|
||||
Iterations, force evaluations = 1000 1943
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.012522 | 0.012522 | 0.012522 | 0.0 | 40.64
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00012209 | 0.00012209 | 0.00012209 | 0.0 | 0.40
|
||||
Output | 0.016563 | 0.016563 | 0.016563 | 0.0 | 53.76
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.001604 | | | 5.20
|
||||
|
||||
Nlocal: 15 ave 15 max 15 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Dynamics
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 3 all xyz 1000 ch4.nve.xyz
|
||||
|
||||
run 100000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.406 | 5.406 | 5.406 Mbytes
|
||||
Step PotEng Temp Press
|
||||
1000 -34.07448 1050 392.66426
|
||||
2000 -34.065618 583.71716 -618.55027
|
||||
3000 -34.063563 475.54605 661.95076
|
||||
4000 -34.06119 350.76183 -449.64687
|
||||
5000 -34.0652 561.71223 -131.2575
|
||||
6000 -34.065798 593.21728 754.38406
|
||||
7000 -34.067408 677.86019 -409.21139
|
||||
8000 -34.065663 586.03411 446.32573
|
||||
9000 -34.06294 442.71136 414.41408
|
||||
10000 -34.060101 293.33406 -1203.0131
|
||||
11000 -34.064946 548.39598 345.29601
|
||||
12000 -34.067323 673.49043 444.55927
|
||||
13000 -34.063275 460.43973 -854.83884
|
||||
14000 -34.064666 533.57265 1542.0127
|
||||
15000 -34.063343 463.97449 -778.73252
|
||||
16000 -34.064462 522.77625 -1.5339614
|
||||
17000 -34.061203 351.37068 -148.19163
|
||||
18000 -34.066534 631.87837 -237.0746
|
||||
19000 -34.065169 560.16772 1360.7348
|
||||
20000 -34.063042 448.13104 -664.72128
|
||||
21000 -34.060696 324.68723 -167.83333
|
||||
22000 -34.065376 570.90279 -831.73853
|
||||
23000 -34.063127 452.61143 766.59984
|
||||
24000 -34.064572 528.62282 -107.80755
|
||||
25000 -34.06584 595.42175 610.33075
|
||||
26000 -34.066886 650.43579 -894.20521
|
||||
27000 -34.062035 395.20224 1754.7666
|
||||
28000 -34.060696 324.66878 -2622.013
|
||||
29000 -34.066777 644.66282 1551.3147
|
||||
30000 -34.066421 625.94614 -507.44173
|
||||
31000 -34.066163 612.36658 610.11907
|
||||
32000 -34.063109 451.70185 -47.463209
|
||||
33000 -34.062833 437.16794 -607.25848
|
||||
34000 -34.061657 375.30056 -158.28097
|
||||
35000 -34.064937 547.86519 272.75585
|
||||
36000 -34.067509 683.23088 359.91072
|
||||
37000 -34.067582 686.96461 -384.97405
|
||||
38000 -34.063213 457.13191 411.86349
|
||||
39000 -34.06272 431.13187 -594.23723
|
||||
40000 -34.062286 408.41212 456.09079
|
||||
41000 -34.064078 502.64096 -1149.8496
|
||||
42000 -34.066408 625.33334 1403.4937
|
||||
43000 -34.065948 601.03876 -773.40678
|
||||
44000 -34.064113 504.49498 179.93456
|
||||
45000 -34.060573 318.11433 223.38679
|
||||
46000 -34.063614 478.24588 -409.99081
|
||||
47000 -34.064814 541.38544 614.25246
|
||||
48000 -34.065602 582.87984 -743.92184
|
||||
49000 -34.063923 494.52673 474.88127
|
||||
50000 -34.064616 530.94533 288.81199
|
||||
51000 -34.062038 395.2991 -480.07513
|
||||
52000 -34.06497 549.5123 -305.53764
|
||||
53000 -34.065578 581.59919 964.80956
|
||||
54000 -34.06766 691.12707 -437.99603
|
||||
55000 -34.064707 535.85658 1058.6734
|
||||
56000 -34.062481 418.58003 -1011.5341
|
||||
57000 -34.064997 551.06731 -32.91724
|
||||
58000 -34.064281 513.25358 374.91628
|
||||
59000 -34.066177 613.1188 -464.85124
|
||||
60000 -34.064718 536.29803 1011.6698
|
||||
61000 -34.065746 590.46955 -1057.9241
|
||||
62000 -34.063253 459.23293 1526.2698
|
||||
63000 -34.062261 407.08636 -1743.6652
|
||||
64000 -34.063835 489.88286 761.60266
|
||||
65000 -34.069569 791.614 323.26812
|
||||
66000 -34.065557 580.45685 874.52459
|
||||
67000 -34.064917 546.77223 -1349.3606
|
||||
68000 -34.062963 443.96697 1178.4319
|
||||
69000 -34.063063 449.26418 -1660.686
|
||||
70000 -34.063597 477.39716 1323.13
|
||||
71000 -34.065424 573.47914 -131.55428
|
||||
72000 -34.065211 562.31067 -415.56361
|
||||
73000 -34.06339 466.38097 724.92885
|
||||
74000 -34.062286 408.34027 -1094.3845
|
||||
75000 -34.065545 579.79767 587.58121
|
||||
76000 -34.066774 644.61685 -357.22241
|
||||
77000 -34.064479 523.74831 1545.6628
|
||||
78000 -34.065506 577.88405 -1013.2409
|
||||
79000 -34.062874 439.24856 240.66725
|
||||
80000 -34.06306 449.09678 -799.14252
|
||||
81000 -34.063338 463.66067 1528.3351
|
||||
82000 -34.066812 646.52985 -1351.1758
|
||||
83000 -34.064724 536.65114 1338.595
|
||||
84000 -34.063774 486.67172 -876.0475
|
||||
85000 -34.06156 370.19256 617.89915
|
||||
86000 -34.063628 478.95398 -134.40164
|
||||
87000 -34.065141 558.60424 -758.03942
|
||||
88000 -34.066732 642.27865 1159.5992
|
||||
89000 -34.067349 674.83453 -301.45201
|
||||
90000 -34.063623 478.69626 386.87752
|
||||
91000 -34.061885 387.30728 -774.32296
|
||||
92000 -34.061363 359.77745 500.06117
|
||||
93000 -34.065724 589.32209 -469.10399
|
||||
94000 -34.065006 551.42796 818.92294
|
||||
95000 -34.06541 572.75191 -677.20865
|
||||
96000 -34.062331 410.64868 1383.8935
|
||||
97000 -34.061499 366.95753 -1715.2058
|
||||
98000 -34.061153 348.68703 353.63545
|
||||
99000 -34.066217 615.27816 193.79593
|
||||
100000 -34.067739 695.36238 205.35389
|
||||
101000 -34.067314 672.94727 929.41223
|
||||
Loop time of 2.23163 on 1 procs for 100000 steps with 15 atoms
|
||||
|
||||
Performance: 19358038.198 fs/day, 0.000 hours/fs, 44810.274 timesteps/s, 672.154 katom-step/s
|
||||
85.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.59187 | 0.59187 | 0.59187 | 0.0 | 26.52
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0061524 | 0.0061524 | 0.0061524 | 0.0 | 0.28
|
||||
Output | 1.5983 | 1.5983 | 1.5983 | 0.0 | 71.62
|
||||
Modify | 0.017759 | 0.017759 | 0.017759 | 0.0 | 0.80
|
||||
Other | | 0.01755 | | | 0.79
|
||||
|
||||
Nlocal: 15 ave 15 max 15 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.4
Normal file
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.4
Normal file
@ -0,0 +1,266 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.ch4
|
||||
Reading data file ...
|
||||
orthogonal box = (-500 -500 -500) to (500 500 500)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
15 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 102
|
||||
ghost atom cutoff = 102
|
||||
binsize = 51, bins = 20 20 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.385 | 5.385 | 5.385 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -27.314082 0 -27.314082 -56588.53
|
||||
1000 0 -34.07448 0 -34.07448 0.39495391
|
||||
Loop time of 0.0230482 on 4 procs for 1000 steps with 15 atoms
|
||||
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-27.3140820331249 -34.0744796901924 -34.0744796901707
|
||||
Force two-norm initial, final = 10.728716 0.00024139276
|
||||
Force max component initial, final = 6.1727999 0.00017091779
|
||||
Final line search alpha, max atom move = 1 0.00017091779
|
||||
Iterations, force evaluations = 1000 1946
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0015331 | 0.0032095 | 0.0046681 | 2.0 | 13.93
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0037211 | 0.0053887 | 0.0069902 | 1.6 | 23.38
|
||||
Output | 0.0062087 | 0.0079064 | 0.011172 | 2.2 | 34.30
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.006544 | | | 28.39
|
||||
|
||||
Nlocal: 3.75 ave 6 max 3 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 11.25 ave 12 max 9 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 26.25 ave 39 max 12 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Dynamics
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 3 all xyz 1000 ch4.nve.xyz
|
||||
|
||||
run 100000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.401 | 5.401 | 5.401 Mbytes
|
||||
Step PotEng Temp Press
|
||||
1000 -34.07448 1050 391.71277
|
||||
2000 -34.065618 583.70724 -617.78946
|
||||
3000 -34.063563 475.53779 661.75865
|
||||
4000 -34.06119 350.74901 -449.8917
|
||||
5000 -34.065201 561.76559 -130.73147
|
||||
6000 -34.065798 593.21893 753.94281
|
||||
7000 -34.067408 677.86552 -409.14034
|
||||
8000 -34.065662 586.02658 446.74947
|
||||
9000 -34.062939 442.6953 413.93386
|
||||
10000 -34.060101 293.35262 -1202.4169
|
||||
11000 -34.064946 548.37877 344.89658
|
||||
12000 -34.067324 673.52389 444.40605
|
||||
13000 -34.063275 460.44923 -854.41022
|
||||
14000 -34.064667 533.59655 1541.2922
|
||||
15000 -34.063344 464.01572 -777.83895
|
||||
16000 -34.064461 522.76554 -2.2050586
|
||||
17000 -34.061202 351.31261 -148.09486
|
||||
18000 -34.066534 631.89021 -236.72076
|
||||
19000 -34.065169 560.16576 1359.8928
|
||||
20000 -34.063042 448.14707 -663.76152
|
||||
21000 -34.060695 324.66945 -168.3252
|
||||
22000 -34.065376 570.90677 -831.8481
|
||||
23000 -34.063127 452.62391 767.31463
|
||||
24000 -34.064572 528.62018 -108.63204
|
||||
25000 -34.06584 595.41818 610.87995
|
||||
26000 -34.066885 650.4263 -894.11862
|
||||
27000 -34.062035 395.1876 1754.1737
|
||||
28000 -34.060697 324.71187 -2621.333
|
||||
29000 -34.066777 644.68166 1550.7046
|
||||
30000 -34.066421 625.9368 -507.12512
|
||||
31000 -34.066163 612.3605 610.12993
|
||||
32000 -34.063108 451.66459 -48.049967
|
||||
33000 -34.062834 437.21062 -606.58502
|
||||
34000 -34.061656 375.26971 -158.76936
|
||||
35000 -34.064938 547.90576 273.26572
|
||||
36000 -34.067508 683.20936 360.05973
|
||||
37000 -34.067582 686.96938 -385.62265
|
||||
38000 -34.063213 457.13708 412.74004
|
||||
39000 -34.06272 431.16474 -595.05437
|
||||
40000 -34.062285 408.38247 456.29631
|
||||
41000 -34.064078 502.65934 -1149.196
|
||||
42000 -34.066408 625.33356 1402.5676
|
||||
43000 -34.065948 601.04311 -772.96544
|
||||
44000 -34.064113 504.47553 179.83988
|
||||
45000 -34.060572 318.08821 222.85125
|
||||
46000 -34.063614 478.25613 -409.06152
|
||||
47000 -34.064813 541.37361 613.37159
|
||||
48000 -34.065602 582.88704 -743.72019
|
||||
49000 -34.063922 494.52189 475.22811
|
||||
50000 -34.064616 530.95516 288.46302
|
||||
51000 -34.062038 395.30091 -479.68548
|
||||
52000 -34.06497 549.50477 -305.82851
|
||||
53000 -34.065577 581.56927 964.95886
|
||||
54000 -34.06766 691.14533 -437.95563
|
||||
55000 -34.064707 535.85441 1058.0886
|
||||
56000 -34.062481 418.62259 -1010.5517
|
||||
57000 -34.064996 551.02074 -33.54291
|
||||
58000 -34.064281 513.27818 375.07194
|
||||
59000 -34.066177 613.11494 -464.71576
|
||||
60000 -34.064718 536.306 1010.9545
|
||||
61000 -34.065746 590.47317 -1056.9192
|
||||
62000 -34.063252 459.22005 1525.6789
|
||||
63000 -34.06226 407.05859 -1743.9974
|
||||
64000 -34.063836 489.91026 762.61836
|
||||
65000 -34.069569 791.63831 322.35333
|
||||
66000 -34.065557 580.46799 875.11714
|
||||
67000 -34.064916 546.74052 -1349.5741
|
||||
68000 -34.062962 443.93438 1178.1978
|
||||
69000 -34.063064 449.3052 -1659.8695
|
||||
70000 -34.063596 477.36452 1322.0559
|
||||
71000 -34.065424 573.49586 -131.11749
|
||||
72000 -34.06521 562.24612 -415.25895
|
||||
73000 -34.06339 466.38351 724.08642
|
||||
74000 -34.062286 408.37673 -1093.6751
|
||||
75000 -34.065545 579.81257 586.8907
|
||||
76000 -34.066774 644.62609 -356.7044
|
||||
77000 -34.064479 523.75235 1545.8498
|
||||
78000 -34.065506 577.88123 -1014.0878
|
||||
79000 -34.062875 439.30997 241.55748
|
||||
80000 -34.06306 449.06553 -799.58139
|
||||
81000 -34.063338 463.64261 1528.4412
|
||||
82000 -34.066812 646.55603 -1350.9377
|
||||
83000 -34.064724 536.63793 1338.2148
|
||||
84000 -34.063774 486.717 -875.60363
|
||||
85000 -34.06156 370.19433 617.85579
|
||||
86000 -34.063628 478.9961 -135.13703
|
||||
87000 -34.065141 558.62541 -756.91518
|
||||
88000 -34.066732 642.27743 1158.5797
|
||||
89000 -34.067351 674.92164 -300.79164
|
||||
90000 -34.063624 478.70378 386.44004
|
||||
91000 -34.061884 387.27577 -774.22945
|
||||
92000 -34.061364 359.79856 500.36442
|
||||
93000 -34.065723 589.31234 -469.57015
|
||||
94000 -34.065006 551.46665 819.01826
|
||||
95000 -34.065409 572.7351 -676.74519
|
||||
96000 -34.06233 410.60509 1382.9732
|
||||
97000 -34.0615 366.99019 -1714.2302
|
||||
98000 -34.061152 348.67783 352.89211
|
||||
99000 -34.066217 615.29222 193.8722
|
||||
100000 -34.067739 695.32836 206.03841
|
||||
101000 -34.067313 672.90918 928.0541
|
||||
Loop time of 1.62544 on 4 procs for 100000 steps with 15 atoms
|
||||
|
||||
Performance: 26577371.575 fs/day, 0.000 hours/fs, 61521.693 timesteps/s, 922.825 katom-step/s
|
||||
93.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.066581 | 0.15332 | 0.25928 | 21.7 | 9.43
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.18521 | 0.29733 | 0.3879 | 16.1 | 18.29
|
||||
Output | 0.66513 | 0.81838 | 1.1333 | 20.4 | 50.35
|
||||
Modify | 0.01285 | 0.014237 | 0.016092 | 1.0 | 0.88
|
||||
Other | | 0.3422 | | | 21.05
|
||||
|
||||
Nlocal: 3.75 ave 5 max 3 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 11.25 ave 12 max 10 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 26.25 ave 47 max 10 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.1
Normal file
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.4
Normal file
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.1
Normal file
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.4
Normal file
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -3,12 +3,11 @@
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
log ${sname}.log
|
||||
variable sname index Si2H6
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
@ -23,7 +22,7 @@ variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
@ -39,12 +38,12 @@ thermo_modify temp effTemp press effPress
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 2 ${sname}.min.xyz
|
||||
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
|
||||
@ -3,18 +3,17 @@
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6.ang
|
||||
log ${sname}.log
|
||||
variable sname index Si2H6.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 529.177249
|
||||
pair_style eff/cut 529.177249 ecp 1 Si
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
@ -23,7 +22,7 @@ variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
@ -39,21 +38,21 @@ thermo_modify temp effTemp press effPress
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 10 ${sname}.min.xyz
|
||||
#dump 1 all xyz 10 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-6 2000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
# Equilibrate at 300K
|
||||
velocity all create 300.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#fix 0 all langevin/eff 300.0 300.0 0.1
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
|
||||
|
||||
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.1
Normal file
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.4
Normal file
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.1
Normal file
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.1
Normal file
@ -0,0 +1,185 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Si2H6
|
||||
Reading data file ...
|
||||
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
22 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 1000.0 ecp 1 Si
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 2
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1002
|
||||
ghost atom cutoff = 1002
|
||||
binsize = 501, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.098 | 6.098 | 6.098 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -8.5010994 -8.5010994 0 5.4885963 1.6463577 -15.636053 0 0 3948.0425 3948.0425
|
||||
2 -8.67691 -8.67691 0 5.5258385 1.589403 -15.792152 0 0 3880.1721 3880.1721
|
||||
4 -8.848848 -8.848848 0 5.5663359 1.5311327 -15.946317 0 0 3788.6697 3788.6697
|
||||
6 -9.0177692 -9.0177692 0 5.6106795 1.4710658 -16.099514 0 0 3671.1737 3671.1737
|
||||
8 -9.185303 -9.185303 0 5.6598348 1.4083124 -16.25345 0 0 3523.4287 3523.4287
|
||||
10 -9.3547798 -9.3547798 0 5.7155927 1.3410774 -16.41145 0 0 3336.9891 3336.9891
|
||||
12 -9.5342746 -9.5342746 0 5.7820671 1.2650232 -16.581365 0 0 3091.6153 3091.6153
|
||||
14 -9.753773 -9.753773 0 5.8743943 1.1639 -16.792067 0 0 2711.1247 2711.1247
|
||||
16 -10.097143 -10.097143 0 6.0386279 0.98467639 -17.120448 0 0 1912.0559 1912.0559
|
||||
18 -10.206415 -10.206415 0 6.0972556 0.92111471 -17.224785 0 0 1604.9272 1604.9272
|
||||
20 -10.28471 -10.28471 0 6.1543746 0.86786676 -17.306951 0 0 1325.3681 1325.3681
|
||||
22 -10.343227 -10.343227 0 6.2122367 0.82042286 -17.375887 0 0 1062.6534 1062.6534
|
||||
24 -10.386164 -10.386164 0 6.2699963 0.77763016 -17.43379 0 0 820.84479 820.84479
|
||||
26 -10.416263 -10.416263 0 6.3255676 0.73934069 -17.481171 0 0 608.7375 608.7375
|
||||
28 -10.436521 -10.436521 0 6.3761026 0.70612619 -17.51875 0 0 434.68899 434.68899
|
||||
30 -10.450247 -10.450247 0 6.4147546 0.68147364 -17.546475 0 0 302.62232 302.62232
|
||||
32 -10.456683 -10.456683 0 6.416721 0.67361461 -17.547019 0 0 223.07929 223.07929
|
||||
34 -10.458069 -10.458069 0 6.3974543 0.66990042 -17.525424 0 0 164.78914 164.78914
|
||||
36 -10.458558 -10.458558 0 6.3763802 0.66472241 -17.49966 0 0 100.618 100.618
|
||||
38 -10.459231 -10.459231 0 6.3293189 0.66038284 -17.448933 0 0 -3.1075375 -3.1075375
|
||||
40 -10.459346 -10.459346 0 6.3132377 0.65807627 -17.43066 0 0 -29.981737 -29.981737
|
||||
42 -10.459366 -10.459366 0 6.3179452 0.65719131 -17.434503 0 0 -45.500522 -45.500522
|
||||
44 -10.459413 -10.459413 0 6.2985544 0.66239121 -17.420359 0 0 14.638842 14.638842
|
||||
46 -10.459499 -10.459499 0 6.3129457 0.65696218 -17.429407 0 0 -46.926115 -46.926115
|
||||
48 -10.459522 -10.459522 0 6.3120038 0.65909539 -17.430621 0 0 -27.058486 -27.058486
|
||||
50 -10.459532 -10.459532 0 6.3113769 0.65958039 -17.430489 0 0 -16.067028 -16.067028
|
||||
52 -10.459536 -10.459536 0 6.3181474 0.65939215 -17.437076 0 0 -15.311526 -15.311526
|
||||
54 -10.459539 -10.459539 0 6.3204818 0.66055005 -17.440571 0 0 -0.10049441 -0.10049441
|
||||
56 -10.459539 -10.459539 0 6.320264 0.6605463 -17.440349 0 0 -0.12138433 -0.12138433
|
||||
58 -10.459539 -10.459539 0 6.3204128 0.66045741 -17.440409 0 0 -1.2175181 -1.2175181
|
||||
60 -10.459539 -10.459539 0 6.3201688 0.66048114 -17.440189 0 0 -0.80979907 -0.80979907
|
||||
62 -10.459539 -10.459539 0 6.3201369 0.6605348 -17.440211 0 0 -0.85945578 -0.85945578
|
||||
64 -10.459539 -10.459539 0 6.3201036 0.66047761 -17.44012 0 0 -0.95534716 -0.95534716
|
||||
66 -10.459539 -10.459539 0 6.3201475 0.66049137 -17.440178 0 0 -0.89220676 -0.89220676
|
||||
68 -10.459539 -10.459539 0 6.3201605 0.6605388 -17.440238 0 0 -0.44630696 -0.44630696
|
||||
70 -10.459539 -10.459539 0 6.3202978 0.66049413 -17.440331 0 0 -0.72919073 -0.72919073
|
||||
72 -10.459539 -10.459539 0 6.3202928 0.66056004 -17.440392 0 0 -0.049410442 -0.049410442
|
||||
74 -10.459539 -10.459539 0 6.3204368 0.66055883 -17.440535 0 0 -0.025063323 -0.025063323
|
||||
76 -10.459539 -10.459539 0 6.3204403 0.66054902 -17.440528 0 0 -0.010779864 -0.010779864
|
||||
78 -10.459539 -10.459539 0 6.3203876 0.66056716 -17.440494 0 0 0.087251782 0.087251782
|
||||
80 -10.459539 -10.459539 0 6.3203944 0.66054525 -17.440479 0 0 -0.13822668 -0.13822668
|
||||
82 -10.459539 -10.459539 0 6.3203511 0.66055332 -17.440443 0 0 -0.043786214 -0.043786214
|
||||
84 -10.459539 -10.459539 0 6.32037 0.66054938 -17.440458 0 0 -0.10833476 -0.10833476
|
||||
86 -10.459539 -10.459539 0 6.3203586 0.66055472 -17.440452 0 0 -0.04772439 -0.04772439
|
||||
88 -10.459539 -10.459539 0 6.3203709 0.66055294 -17.440463 0 0 -0.055815521 -0.055815521
|
||||
Loop time of 0.00236996 on 1 procs for 88 steps with 22 atoms
|
||||
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-8.50109938620961 -10.4595390706544 -10.459539070672
|
||||
Force two-norm initial, final = 3.2945156 4.8001667e-06
|
||||
Force max component initial, final = 1.8019385 2.1391495e-06
|
||||
Final line search alpha, max atom move = 1 2.1391495e-06
|
||||
Iterations, force evaluations = 88 127
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0019013 | 0.0019013 | 0.0019013 | 0.0 | 80.23
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.926e-06 | 7.926e-06 | 7.926e-06 | 0.0 | 0.33
|
||||
Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 11.64
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0001848 | | | 7.80
|
||||
|
||||
Nlocal: 22 ave 22 max 22 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 231 ave 231 max 231 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 231
|
||||
Ave neighs/atom = 10.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
Total wall time: 0:00:00
|
||||
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.4
Normal file
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.4
Normal file
@ -0,0 +1,185 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Si2H6
|
||||
Reading data file ...
|
||||
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
22 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style eff/cut 1000.0 ecp 1 Si
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 2
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1002
|
||||
ghost atom cutoff = 1002
|
||||
binsize = 501, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.113 | 6.113 | 6.113 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -8.5010994 -8.5010994 0 5.4885963 1.6463577 -15.636053 0 0 3948.0425 3948.0425
|
||||
2 -8.67691 -8.67691 0 5.5258385 1.589403 -15.792152 0 0 3880.1721 3880.1721
|
||||
4 -8.848848 -8.848848 0 5.5663359 1.5311327 -15.946317 0 0 3788.6697 3788.6697
|
||||
6 -9.0177692 -9.0177692 0 5.6106795 1.4710658 -16.099514 0 0 3671.1737 3671.1737
|
||||
8 -9.185303 -9.185303 0 5.6598348 1.4083124 -16.25345 0 0 3523.4287 3523.4287
|
||||
10 -9.3547798 -9.3547798 0 5.7155927 1.3410774 -16.41145 0 0 3336.9891 3336.9891
|
||||
12 -9.5342746 -9.5342746 0 5.7820671 1.2650232 -16.581365 0 0 3091.6153 3091.6153
|
||||
14 -9.753773 -9.753773 0 5.8743943 1.1639 -16.792067 0 0 2711.1247 2711.1247
|
||||
16 -10.097143 -10.097143 0 6.0386279 0.98467639 -17.120448 0 0 1912.0559 1912.0559
|
||||
18 -10.206415 -10.206415 0 6.0972556 0.92111471 -17.224785 0 0 1604.9272 1604.9272
|
||||
20 -10.28471 -10.28471 0 6.1543746 0.86786676 -17.306951 0 0 1325.3681 1325.3681
|
||||
22 -10.343227 -10.343227 0 6.2122367 0.82042286 -17.375887 0 0 1062.6534 1062.6534
|
||||
24 -10.386164 -10.386164 0 6.2699963 0.77763016 -17.43379 0 0 820.84479 820.84479
|
||||
26 -10.416263 -10.416263 0 6.3255676 0.73934069 -17.481171 0 0 608.7375 608.7375
|
||||
28 -10.436521 -10.436521 0 6.3761026 0.70612619 -17.51875 0 0 434.68899 434.68899
|
||||
30 -10.450247 -10.450247 0 6.4147546 0.68147364 -17.546475 0 0 302.62232 302.62232
|
||||
32 -10.456683 -10.456683 0 6.416721 0.67361461 -17.547019 0 0 223.07929 223.07929
|
||||
34 -10.458069 -10.458069 0 6.3974543 0.66990042 -17.525424 0 0 164.78914 164.78914
|
||||
36 -10.458558 -10.458558 0 6.3763802 0.66472241 -17.49966 0 0 100.618 100.618
|
||||
38 -10.459231 -10.459231 0 6.3293189 0.66038284 -17.448933 0 0 -3.1075375 -3.1075375
|
||||
40 -10.459346 -10.459346 0 6.3132377 0.65807627 -17.43066 0 0 -29.981737 -29.981737
|
||||
42 -10.459366 -10.459366 0 6.3179452 0.65719131 -17.434503 0 0 -45.500522 -45.500522
|
||||
44 -10.459413 -10.459413 0 6.2985544 0.66239121 -17.420359 0 0 14.638842 14.638842
|
||||
46 -10.459499 -10.459499 0 6.3129457 0.65696218 -17.429407 0 0 -46.926115 -46.926115
|
||||
48 -10.459522 -10.459522 0 6.3120038 0.65909539 -17.430621 0 0 -27.058486 -27.058486
|
||||
50 -10.459532 -10.459532 0 6.3113769 0.65958039 -17.430489 0 0 -16.067028 -16.067028
|
||||
52 -10.459536 -10.459536 0 6.3181474 0.65939215 -17.437076 0 0 -15.311525 -15.311525
|
||||
54 -10.459539 -10.459539 0 6.3204818 0.66055005 -17.440571 0 0 -0.1004938 -0.1004938
|
||||
56 -10.459539 -10.459539 0 6.320264 0.6605463 -17.440349 0 0 -0.12138436 -0.12138436
|
||||
58 -10.459539 -10.459539 0 6.3204128 0.66045741 -17.440409 0 0 -1.2175176 -1.2175176
|
||||
60 -10.459539 -10.459539 0 6.3201688 0.66048114 -17.440189 0 0 -0.80979946 -0.80979946
|
||||
62 -10.459539 -10.459539 0 6.3201369 0.6605348 -17.440211 0 0 -0.85945162 -0.85945162
|
||||
64 -10.459539 -10.459539 0 6.3201036 0.66047761 -17.44012 0 0 -0.95534903 -0.95534903
|
||||
66 -10.459539 -10.459539 0 6.3201475 0.66049137 -17.440178 0 0 -0.89220297 -0.89220297
|
||||
68 -10.459539 -10.459539 0 6.3201605 0.6605388 -17.440238 0 0 -0.44631358 -0.44631358
|
||||
70 -10.459539 -10.459539 0 6.3202978 0.66049413 -17.440331 0 0 -0.72919322 -0.72919322
|
||||
72 -10.459539 -10.459539 0 6.3202928 0.66056005 -17.440392 0 0 -0.049401694 -0.049401694
|
||||
74 -10.459539 -10.459539 0 6.3204368 0.66055883 -17.440535 0 0 -0.025056381 -0.025056381
|
||||
76 -10.459539 -10.459539 0 6.3204403 0.66054902 -17.440528 0 0 -0.010774653 -0.010774653
|
||||
78 -10.459539 -10.459539 0 6.3203876 0.66056716 -17.440494 0 0 0.087250755 0.087250755
|
||||
80 -10.459539 -10.459539 0 6.3203944 0.66054525 -17.440479 0 0 -0.13822694 -0.13822694
|
||||
82 -10.459539 -10.459539 0 6.3203511 0.66055332 -17.440443 0 0 -0.043784806 -0.043784806
|
||||
84 -10.459539 -10.459539 0 6.32037 0.66054937 -17.440458 0 0 -0.10833935 -0.10833935
|
||||
86 -10.459539 -10.459539 0 6.3203586 0.66055472 -17.440452 0 0 -0.047719128 -0.047719128
|
||||
88 -10.459539 -10.459539 0 6.3203709 0.66055294 -17.440463 0 0 -0.055818341 -0.055818341
|
||||
Loop time of 0.00213866 on 4 procs for 88 steps with 22 atoms
|
||||
|
||||
95.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-8.50109938620958 -10.4595390706543 -10.459539070672
|
||||
Force two-norm initial, final = 3.2945156 4.7997573e-06
|
||||
Force max component initial, final = 1.8019385 2.1386971e-06
|
||||
Final line search alpha, max atom move = 1 2.1386971e-06
|
||||
Iterations, force evaluations = 88 127
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00027642 | 0.00052972 | 0.00096856 | 0.0 | 24.77
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00035997 | 0.00081245 | 0.0010746 | 0.0 | 37.99
|
||||
Output | 0.00037064 | 0.00039193 | 0.00045231 | 0.0 | 18.33
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0004046 | | | 18.92
|
||||
|
||||
Nlocal: 5.5 ave 7 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Nghost: 16.5 ave 19 max 15 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 57.75 ave 109 max 29 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 231
|
||||
Ave neighs/atom = 10.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,2 +1,3 @@
|
||||
*.csv
|
||||
*.txt
|
||||
*.lammpstrj
|
||||
|
||||
@ -17,14 +17,22 @@ q_ref = float(ref_line[3])
|
||||
inv11_ref = float(ref_line[4])
|
||||
inv12_ref = float(ref_line[5])
|
||||
b1_ref = float(ref_line[6])
|
||||
felec1_ref = float(ref_line[8])
|
||||
felyt1_ref = float(ref_line[10])
|
||||
press_ref = float(ref_line[12])
|
||||
|
||||
# out.csv
|
||||
with open(sys.argv[2]) as f:
|
||||
out_line = f.readlines()[-1].split(", ")
|
||||
e_out = float(out_line[0])
|
||||
q_out = float(out_line[1])
|
||||
press_out = float(out_line[2])
|
||||
|
||||
out_lines = [("energy", e_ref, e_out), ("charge", q_ref, q_out)]
|
||||
out_lines = [
|
||||
("energy", e_ref, e_out),
|
||||
("charge", q_ref, q_out),
|
||||
("pressure", press_ref, press_out),
|
||||
]
|
||||
|
||||
# vec.csv
|
||||
vec_file = "vec.csv"
|
||||
@ -44,6 +52,14 @@ if op.isfile(inv_file):
|
||||
inv12_out = float(inv_line[1])
|
||||
out_lines.append(("inv11", inv11_ref, inv11_out))
|
||||
|
||||
# forces.lammpstrj
|
||||
force_file = "forces.lammpstrj"
|
||||
with open(force_file) as f:
|
||||
lines = f.readlines()[9:]
|
||||
for name, i, f_ref in [("felec1", "1", felec1_ref), ("felyt1", "3", felyt1_ref)]:
|
||||
f_out = next(float(y[3]) for x in lines if (y := x.split()) and y[0] == i)
|
||||
out_lines.append((name, f_ref, f_out))
|
||||
|
||||
lines = []
|
||||
for label, ref, out in out_lines:
|
||||
error = rel_error(out, ref)
|
||||
|
||||
@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
|
||||
fix feta all property/atom d_eta ghost on
|
||||
set group bot d_eta 0.5
|
||||
set group top d_eta 3.0
|
||||
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6
|
||||
fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta algo cg 1e-6
|
||||
|
||||
run 0
|
||||
|
||||
|
||||
@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
|
||||
fix feta all property/atom d_eta ghost on
|
||||
set group bot d_eta 0.5
|
||||
set group top d_eta 3.0
|
||||
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
|
||||
fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
|
||||
|
||||
run 0
|
||||
|
||||
|
||||
@ -1,12 +1,17 @@
|
||||
#!/usr/bin/env python3
|
||||
|
||||
import time
|
||||
|
||||
import numpy as np
|
||||
from scipy.special import erf
|
||||
|
||||
SQRT2 = np.sqrt(2)
|
||||
SQRTPI_INV = 1 / np.sqrt(np.pi)
|
||||
COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units
|
||||
QE2F = 23.060549
|
||||
NKTV2P = 68568.415 # pressure in 'real' units
|
||||
LENGTH = 10000 # convergence parameter
|
||||
LZ = 20
|
||||
|
||||
|
||||
def lattice(length):
|
||||
@ -26,6 +31,25 @@ def b_element(r, q, eta):
|
||||
return q * erf(eta * r) / r
|
||||
|
||||
|
||||
def force_gauss(r, qq, eta):
|
||||
etar = eta * r
|
||||
return (qq / np.square(r)) * (
|
||||
erf(etar) - 2 * etar * SQRTPI_INV * np.exp(-np.square(etar))
|
||||
)
|
||||
|
||||
|
||||
def force_point(r, qq):
|
||||
return qq / np.square(r)
|
||||
|
||||
|
||||
def force_component(dx, d, qq, eta=None):
|
||||
if eta:
|
||||
return np.sum(dx / d * force_gauss(d, qq, eta))
|
||||
else:
|
||||
return np.sum(dx / d * force_point(d, qq))
|
||||
|
||||
|
||||
time_start = time.perf_counter()
|
||||
a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2)
|
||||
x_elec = [-2, 2]
|
||||
x_elyt = [-1, 1]
|
||||
@ -36,8 +60,20 @@ v = np.array([-0.5, 0.5]) * (QE2F / COULOMB)
|
||||
# distances to images within electrode and to opposite electrode
|
||||
distances = a * np.linalg.norm(lattice(LENGTH), axis=1)
|
||||
opposite_distances = np.sqrt(np.square(distances) + distance_plates**2)
|
||||
image_distances = []
|
||||
for x in x_elec:
|
||||
image_distances.append([])
|
||||
for y in x_elyt:
|
||||
image_distances[-1].append(np.sqrt(np.square(distances) + np.abs(y - x) ** 2))
|
||||
image_elyt_distances = [[None for _ in range(len(x_elyt))] for _ in range(len(x_elyt))]
|
||||
for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
|
||||
for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
|
||||
image_elyt_distances[i][j] = np.sqrt(
|
||||
np.square(distances) + np.abs(xj - xi) ** 2
|
||||
)
|
||||
|
||||
for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
|
||||
# for name, eta_elec in [("", [2.0, 2.0])]:
|
||||
eta_mix = np.prod(eta_elec) / np.sqrt(np.sum(np.square(eta_elec)))
|
||||
# self interaction and within original box
|
||||
A_11 = np.sqrt(2 / np.pi) * eta_elec[0]
|
||||
@ -55,22 +91,18 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
|
||||
|
||||
# electrode-electrolyte interaction
|
||||
b = []
|
||||
for x, eta in zip(x_elec, eta_elec):
|
||||
for i, (x, eta) in enumerate(zip(x_elec, eta_elec)):
|
||||
bi = 0
|
||||
for y, q in zip(x_elyt, q_elyt):
|
||||
d = abs(y - x)
|
||||
bi += b_element(d, q, eta)
|
||||
image_distances = np.sqrt(np.square(distances) + d**2)
|
||||
bi += 4 * np.sum(b_element(image_distances, q, eta))
|
||||
for j, (y, q) in enumerate(zip(x_elyt, q_elyt)):
|
||||
bi += b_element(np.abs(y - x), q, eta)
|
||||
bi += 4 * np.sum(b_element(image_distances[i][j], q, eta))
|
||||
b.append(bi)
|
||||
b = np.array(b)
|
||||
|
||||
# electrolyte-electrolyte energy
|
||||
elyt_11 = 4 * np.sum(1 / distances)
|
||||
distance_elyt = x_elyt[1] - x_elyt[0]
|
||||
elyt_12 = 1 / distance_elyt + 4 * np.sum(
|
||||
1 / np.sqrt(np.square(distances) + distance_elyt**2)
|
||||
)
|
||||
elyt_12 = 1 / distance_elyt + 4 * np.sum(1 / image_elyt_distances[0][1])
|
||||
elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]])
|
||||
energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt))
|
||||
|
||||
@ -78,9 +110,48 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
|
||||
q = np.dot(inv, v - b)
|
||||
energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt)
|
||||
|
||||
# forces in out-of-plane direction
|
||||
f_elec = np.zeros(len(x_elec))
|
||||
f_elyt = np.zeros(len(x_elyt))
|
||||
# electrode-electrode
|
||||
dx = x_elec[1] - x_elec[0]
|
||||
fij_box = force_component(dx, np.abs(dx), q[0] * q[1], eta_mix)
|
||||
fij_img = 4 * force_component(dx, opposite_distances, q[0] * q[1], eta_mix)
|
||||
f_elec[0] -= fij_box + fij_img
|
||||
f_elec[1] += fij_box + fij_img
|
||||
# electrode-electrolyte
|
||||
for i, (xi, qi, etai) in enumerate(zip(x_elec, q, eta_elec)):
|
||||
for j, (xj, qj) in enumerate(zip(x_elyt, q_elyt)):
|
||||
dx = xj - xi
|
||||
fij_box = force_component(dx, np.abs(dx), qi * qj, etai)
|
||||
fij_img = 4 * force_component(dx, image_distances[i][j], qi * qj, etai)
|
||||
f_elec[i] -= fij_box + fij_img
|
||||
f_elyt[j] += fij_box + fij_img
|
||||
# electrolyte-electrolyte
|
||||
for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
|
||||
for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
|
||||
dx = xj - xi
|
||||
fij_box = force_component(dx, np.abs(dx), qi * qj)
|
||||
fij_img = 4 * force_component(dx, image_elyt_distances[i][j], qi * qj)
|
||||
f_elyt[i] -= fij_img + fij_box
|
||||
f_elyt[j] += fij_img + fij_box
|
||||
# force units
|
||||
assert np.abs(np.sum(f_elec) + np.sum(f_elyt)) < 1e-8
|
||||
f_elec *= COULOMB
|
||||
f_elyt *= COULOMB
|
||||
|
||||
# Virial
|
||||
volume = a**2 * LZ
|
||||
virial = 0.0
|
||||
for x, f in [(x_elec, f_elec), (x_elyt, f_elyt)]:
|
||||
virial += np.dot(x, f)
|
||||
pressure = NKTV2P * virial / volume
|
||||
|
||||
with open(f"plate_cap{name}.csv", "w") as f:
|
||||
f.write(
|
||||
"length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A\n"
|
||||
"length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A"
|
||||
+ ", b1 / e/A, b2 / e/A, felec1 / kcal/mol/A, felec2 / kcal/mol/A"
|
||||
+ ", felyt1 / kcal/mol/A, felyt2 / kcal/mol/A, press\n"
|
||||
)
|
||||
f.write(
|
||||
", ".join(
|
||||
@ -93,7 +164,14 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
|
||||
f"{inv[0, 1]:.10f}",
|
||||
f"{b[0]:.8f}",
|
||||
f"{b[1]:.8f}",
|
||||
f"{f_elec[0]:.5f}",
|
||||
f"{f_elec[1]:.5f}",
|
||||
f"{f_elyt[0]:.5f}",
|
||||
f"{f_elyt[1]:.5f}",
|
||||
f"{pressure:.2f}",
|
||||
]
|
||||
)
|
||||
+ "\n"
|
||||
)
|
||||
time_end = time.perf_counter()
|
||||
print(f"{time_end - time_start:0.4f} seconds")
|
||||
|
||||
@ -19,4 +19,8 @@ compute qtop top reduce sum v_q
|
||||
compute compute_pe all pe
|
||||
variable vpe equal c_compute_pe
|
||||
variable charge equal c_qtop
|
||||
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
|
||||
compute press all pressure NULL virial
|
||||
variable p3 equal c_press[3]
|
||||
fix fxprint all print 1 "${vpe}, ${charge}, ${p3}" file "out.csv"
|
||||
|
||||
dump dump_forces all custom 1 forces.lammpstrj id fx fy fz
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -42,7 +42,11 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
|
||||
|
||||
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
|
||||
fix fxforce_wa wall setforce 0.0 0.0 NULL
|
||||
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
|
||||
variable atm equal 1/68568.415 # 1/force->nktv2p
|
||||
variable area equal (xhi-xlo)*(yhi-ylo)
|
||||
variable wall_force equal -v_atm*v_area/count(wall)
|
||||
print "Wall force per atom: ${wall_force}"
|
||||
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
|
||||
fix fxdrag wall viscous 100
|
||||
fix fxrigid wall rigid/nve single
|
||||
|
||||
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (3 Nov 2022)
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# The intention is to find the average position of one wall at atmospheric
|
||||
# pressure. The output is the wall position over time which can be used to
|
||||
# find the average position for a run with fixed wall position.
|
||||
@ -40,8 +41,8 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
# ----------------- Settings Section -----------------
|
||||
|
||||
@ -77,7 +78,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
|
||||
|
||||
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
|
||||
fix fxforce_wa wall setforce 0.0 0.0 NULL
|
||||
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
|
||||
variable atm equal 1/68568.415 # 1/force->nktv2p
|
||||
variable area equal (xhi-xlo)*(yhi-ylo)
|
||||
variable wall_force equal -v_atm*v_area/count(wall)
|
||||
print "Wall force per atom: ${wall_force}"
|
||||
Wall force per atom: -0.000109285996244287
|
||||
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
|
||||
fix fxpressure wall aveforce 0 0 -0.000109285996244287
|
||||
fix fxdrag wall viscous 100
|
||||
fix fxrigid wall rigid/nve single
|
||||
1 rigid bodies with 48 atoms
|
||||
@ -134,7 +141,7 @@ PPPM/electrode initialization ...
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.02930901
|
||||
estimated relative force accuracy = 8.8263214e-05
|
||||
using double precision MKL FFT
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 15884 6480
|
||||
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
@ -157,54 +164,54 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes
|
||||
Step c_temp_mobile c_qwa c_qau v_top_wall
|
||||
0 303.38967 -0.042963484 0.042963484 21.4018
|
||||
5000 285.08828 -0.26105255 0.26105255 25.155629
|
||||
10000 323.19176 -0.26264003 0.26264003 24.541676
|
||||
15000 310.479 -0.27318148 0.27318148 23.141522
|
||||
20000 295.18544 -0.11313444 0.11313444 23.828735
|
||||
25000 295.38607 -0.25433086 0.25433086 23.673314
|
||||
30000 288.0613 -0.30099901 0.30099901 23.438086
|
||||
35000 278.5591 -0.15823576 0.15823576 24.311915
|
||||
40000 303.95751 -0.19941381 0.19941381 23.69594
|
||||
45000 279.026 -0.1659962 0.1659962 23.588604
|
||||
50000 298.79278 -0.28866703 0.28866703 23.372508
|
||||
55000 301.03353 -0.078370381 0.078370381 23.192985
|
||||
60000 306.77965 -0.12807205 0.12807205 23.968574
|
||||
65000 309.86008 -0.27162663 0.27162663 23.616704
|
||||
70000 287.31116 -0.029751882 0.029751882 23.667495
|
||||
75000 312.48654 -0.10759866 0.10759866 23.504105
|
||||
80000 309.94267 -0.2558548 0.2558548 23.810576
|
||||
85000 328.04389 -0.1575471 0.1575471 24.013437
|
||||
90000 302.9806 -0.032002164 0.032002164 24.264432
|
||||
95000 294.20804 -0.27797238 0.27797238 23.291758
|
||||
100000 307.63019 -0.19047448 0.19047448 23.632147
|
||||
Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms
|
||||
5000 311.85363 0.03543775 -0.03543775 24.79665
|
||||
10000 285.91321 -0.16873703 0.16873703 23.103088
|
||||
15000 295.39476 -0.44424612 0.44424612 23.767107
|
||||
20000 296.12969 -0.14120993 0.14120993 23.96361
|
||||
25000 306.59629 -0.29333182 0.29333182 23.884488
|
||||
30000 297.98559 -0.10749684 0.10749684 23.73316
|
||||
35000 297.98503 -0.11809975 0.11809975 23.984669
|
||||
40000 300.26292 -0.32784184 0.32784184 23.462748
|
||||
45000 295.68441 -0.25940165 0.25940165 23.516403
|
||||
50000 315.12883 -0.36037614 0.36037614 23.627879
|
||||
55000 290.55151 -0.0032838106 0.0032838106 23.684931
|
||||
60000 316.4625 -0.17245368 0.17245368 24.126883
|
||||
65000 296.79343 -0.054061851 0.054061851 23.695094
|
||||
70000 305.99923 -0.11363801 0.11363801 23.55476
|
||||
75000 297.40131 -0.27054153 0.27054153 23.928994
|
||||
80000 306.54811 -0.25409719 0.25409719 23.869448
|
||||
85000 303.95231 -0.17895561 0.17895561 23.658833
|
||||
90000 313.43739 -0.059036514 0.059036514 23.36056
|
||||
95000 290.3077 -0.31394478 0.31394478 23.885538
|
||||
100000 297.5156 -0.30730083 0.30730083 23.511674
|
||||
Loop time of 1586.06 on 1 procs for 100000 steps with 726 atoms
|
||||
|
||||
Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 katom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 10.895 ns/day, 2.203 hours/ns, 63.049 timesteps/s, 45.774 katom-step/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 190.47 | 190.47 | 190.47 | 0.0 | 35.88
|
||||
Bond | 0.10754 | 0.10754 | 0.10754 | 0.0 | 0.02
|
||||
Kspace | 73.179 | 73.179 | 73.179 | 0.0 | 13.79
|
||||
Neigh | 24.209 | 24.209 | 24.209 | 0.0 | 4.56
|
||||
Comm | 1.6857 | 1.6857 | 1.6857 | 0.0 | 0.32
|
||||
Output | 0.0016861 | 0.0016861 | 0.0016861 | 0.0 | 0.00
|
||||
Modify | 240.23 | 240.23 | 240.23 | 0.0 | 45.26
|
||||
Other | | 0.9595 | | | 0.18
|
||||
Pair | 460.91 | 460.91 | 460.91 | 0.0 | 29.06
|
||||
Bond | 0.047873 | 0.047873 | 0.047873 | 0.0 | 0.00
|
||||
Kspace | 341.4 | 341.4 | 341.4 | 0.0 | 21.53
|
||||
Neigh | 52.868 | 52.868 | 52.868 | 0.0 | 3.33
|
||||
Comm | 5.2321 | 5.2321 | 5.2321 | 0.0 | 0.33
|
||||
Output | 0.00099102 | 0.00099102 | 0.00099102 | 0.0 | 0.00
|
||||
Modify | 724.63 | 724.63 | 724.63 | 0.0 | 45.69
|
||||
Other | | 0.9741 | | | 0.06
|
||||
|
||||
Nlocal: 726 ave 726 max 726 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2335 ave 2335 max 2335 min
|
||||
Nghost: 2336 ave 2336 max 2336 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 120271 ave 120271 max 120271 min
|
||||
Neighs: 120321 ave 120321 max 120321 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 120271
|
||||
Ave neighs/atom = 165.66253
|
||||
Total # of neighbors = 120321
|
||||
Ave neighs/atom = 165.7314
|
||||
Ave special neighs/atom = 1.7355372
|
||||
Neighbor list builds = 7722
|
||||
Neighbor list builds = 7670
|
||||
Dangerous builds = 0
|
||||
write_data "data.piston.final"
|
||||
System init for write_data ...
|
||||
@ -213,11 +220,11 @@ PPPM/electrode initialization ...
|
||||
G vector (1/distance) = 0.32814871
|
||||
grid = 12 15 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.029311365
|
||||
estimated relative force accuracy = 8.8270304e-05
|
||||
using double precision MKL FFT
|
||||
estimated absolute RMS force accuracy = 0.029311329
|
||||
estimated relative force accuracy = 8.8270197e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 15884 6480
|
||||
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
|
||||
Average conjugate gradient steps: 1.981
|
||||
Total wall time: 0:08:50
|
||||
Total wall time: 0:26:26
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (3 Nov 2022)
|
||||
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# The intention is to find the average position of one wall at atmospheric
|
||||
# pressure. The output is the wall position over time which can be used to
|
||||
# find the average position for a run with fixed wall position.
|
||||
@ -41,8 +42,8 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.017 seconds
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
# ----------------- Settings Section -----------------
|
||||
|
||||
@ -66,7 +67,7 @@ Finding SHAKE clusters ...
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
210 = # of frozen angles
|
||||
find clusters CPU = 0.002 seconds
|
||||
find clusters CPU = 0.000 seconds
|
||||
pair_modify mix arithmetic
|
||||
|
||||
# ----------------- Run Section -----------------
|
||||
@ -78,7 +79,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
|
||||
|
||||
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
|
||||
fix fxforce_wa wall setforce 0.0 0.0 NULL
|
||||
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
|
||||
variable atm equal 1/68568.415 # 1/force->nktv2p
|
||||
variable area equal (xhi-xlo)*(yhi-ylo)
|
||||
variable wall_force equal -v_atm*v_area/count(wall)
|
||||
print "Wall force per atom: ${wall_force}"
|
||||
Wall force per atom: -0.000109285996244287
|
||||
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
|
||||
fix fxpressure wall aveforce 0 0 -0.000109285996244287
|
||||
fix fxdrag wall viscous 100
|
||||
fix fxrigid wall rigid/nve single
|
||||
1 rigid bodies with 48 atoms
|
||||
@ -135,7 +142,7 @@ PPPM/electrode initialization ...
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.02930901
|
||||
estimated relative force accuracy = 8.8263214e-05
|
||||
using double precision MKL FFT
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 8512 2880
|
||||
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
@ -158,54 +165,54 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.22 | 10.41 Mbytes
|
||||
Step c_temp_mobile c_qwa c_qau v_top_wall
|
||||
0 303.38967 -0.042963484 0.042963484 21.4018
|
||||
5000 292.03027 -0.19040435 0.19040435 24.581338
|
||||
10000 309.52764 -0.48308301 0.48308301 23.776985
|
||||
15000 295.00243 -0.16591109 0.16591109 23.672038
|
||||
20000 293.5536 -0.086669084 0.086669084 23.426455
|
||||
25000 303.0079 -0.16488112 0.16488112 23.862966
|
||||
30000 306.31463 -0.23192653 0.23192653 23.819882
|
||||
35000 303.66268 -0.2317907 0.2317907 23.495344
|
||||
40000 301.39435 -0.34661329 0.34661329 23.657835
|
||||
45000 291.61205 -0.30539427 0.30539427 23.437303
|
||||
50000 298.65319 -0.096107034 0.096107034 23.57809
|
||||
55000 282.65069 -0.14943539 0.14943539 23.823728
|
||||
60000 310.64182 -0.17418813 0.17418813 23.286959
|
||||
65000 308.47141 -0.02075662 0.02075662 23.91313
|
||||
70000 292.5186 -0.080163162 0.080163162 23.96283
|
||||
75000 270.13928 -0.029528648 0.029528648 23.488972
|
||||
80000 322.10914 0.030761045 -0.030761045 23.47592
|
||||
85000 310.60347 -0.24069996 0.24069996 23.987091
|
||||
90000 294.35695 -0.070458235 0.070458235 23.397929
|
||||
95000 308.69043 -0.2652581 0.2652581 23.473813
|
||||
100000 318.71883 0.024035956 -0.024035956 23.449863
|
||||
Loop time of 590.232 on 4 procs for 100000 steps with 726 atoms
|
||||
5000 291.6303 -0.1820085 0.1820085 24.641399
|
||||
10000 299.42886 -0.19823095 0.19823095 23.820522
|
||||
15000 288.23071 -0.065261869 0.065261869 23.360845
|
||||
20000 299.4644 -0.042993777 0.042993777 23.987554
|
||||
25000 304.26497 -0.15665293 0.15665293 23.729006
|
||||
30000 292.29674 -0.25142779 0.25142779 23.960725
|
||||
35000 295.57492 -0.01269228 0.01269228 23.445383
|
||||
40000 303.38438 -0.13941727 0.13941727 23.517483
|
||||
45000 302.211 -0.19589892 0.19589892 23.704043
|
||||
50000 281.64939 -0.18057298 0.18057298 23.542137
|
||||
55000 274.90565 -0.15453379 0.15453379 23.734347
|
||||
60000 290.70459 -0.27977436 0.27977436 23.835365
|
||||
65000 293.42241 -0.2454241 0.2454241 23.59269
|
||||
70000 295.20229 -0.041314995 0.041314995 23.73856
|
||||
75000 297.79519 -0.11231755 0.11231755 23.57262
|
||||
80000 285.17858 -0.070796508 0.070796508 23.817135
|
||||
85000 311.71609 -0.068920177 0.068920177 23.861127
|
||||
90000 287.80446 -0.19183387 0.19183387 23.369393
|
||||
95000 309.43345 -0.15238671 0.15238671 23.597792
|
||||
100000 294.12422 -0.14284353 0.14284353 23.526286
|
||||
Loop time of 876.546 on 4 procs for 100000 steps with 726 atoms
|
||||
|
||||
Performance: 29.277 ns/day, 0.820 hours/ns, 169.425 timesteps/s, 123.003 katom-step/s
|
||||
72.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 19.714 ns/day, 1.217 hours/ns, 114.084 timesteps/s, 82.825 katom-step/s
|
||||
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 57.391 | 75.867 | 96.292 | 212.1 | 12.85
|
||||
Bond | 0.10177 | 0.11042 | 0.12415 | 2.7 | 0.02
|
||||
Kspace | 102.79 | 123.16 | 141.5 | 165.7 | 20.87
|
||||
Neigh | 12.808 | 12.895 | 12.982 | 2.3 | 2.18
|
||||
Comm | 18.885 | 19.973 | 21.064 | 24.0 | 3.38
|
||||
Output | 0.0022573 | 0.0022749 | 0.0023225 | 0.1 | 0.00
|
||||
Modify | 355.89 | 356.74 | 357.61 | 4.2 | 60.44
|
||||
Other | | 1.478 | | | 0.25
|
||||
Pair | 123.63 | 171.23 | 215.73 | 336.6 | 19.53
|
||||
Bond | 0.068261 | 0.075883 | 0.081822 | 1.9 | 0.01
|
||||
Kspace | 187.59 | 231.71 | 279.01 | 287.1 | 26.43
|
||||
Neigh | 29.28 | 29.462 | 29.637 | 2.5 | 3.36
|
||||
Comm | 12.544 | 13.731 | 14.929 | 29.1 | 1.57
|
||||
Output | 0.0010182 | 0.0014585 | 0.0016071 | 0.7 | 0.00
|
||||
Modify | 428.74 | 429.25 | 429.74 | 2.3 | 48.97
|
||||
Other | | 1.092 | | | 0.12
|
||||
|
||||
Nlocal: 181.5 ave 207 max 169 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
Nghost: 1961.5 ave 1984 max 1926 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 30051 ave 41646 max 20775 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nlocal: 181.5 ave 195 max 166 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 1955.5 ave 1978 max 1931 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 30343 ave 39847 max 20428 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 120204
|
||||
Ave neighs/atom = 165.57025
|
||||
Total # of neighbors = 121372
|
||||
Ave neighs/atom = 167.17906
|
||||
Ave special neighs/atom = 1.7355372
|
||||
Neighbor list builds = 7663
|
||||
Neighbor list builds = 7698
|
||||
Dangerous builds = 0
|
||||
write_data "data.piston.final"
|
||||
System init for write_data ...
|
||||
@ -214,11 +221,11 @@ PPPM/electrode initialization ...
|
||||
G vector (1/distance) = 0.32814871
|
||||
grid = 12 15 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.029311028
|
||||
estimated relative force accuracy = 8.8269289e-05
|
||||
using double precision MKL FFT
|
||||
estimated absolute RMS force accuracy = 0.029310954
|
||||
estimated relative force accuracy = 8.8269069e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 8512 2880
|
||||
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
|
||||
Average conjugate gradient steps: 1.982
|
||||
Total wall time: 0:09:50
|
||||
Average conjugate gradient steps: 1.981
|
||||
Total wall time: 0:14:36
|
||||
1
examples/PACKAGES/electron_stopping/AlCu.eam.alloy
Symbolic link
1
examples/PACKAGES/electron_stopping/AlCu.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/AlCu.eam.alloy
|
||||
1
examples/PACKAGES/electron_stopping/SiC.tersoff.zbl
Symbolic link
1
examples/PACKAGES/electron_stopping/SiC.tersoff.zbl
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/SiC.tersoff.zbl
|
||||
@ -12,8 +12,8 @@ region box block -10 10 -10 10 -10 10
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * AlCu.eam.alloy Al Cu
|
||||
|
||||
mass 1 26.982
|
||||
mass 2 63.546
|
||||
|
||||
@ -13,7 +13,7 @@ create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style tersoff/zbl
|
||||
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
|
||||
pair_coeff * * SiC.tersoff.zbl Si
|
||||
|
||||
mass 1 28.0855
|
||||
|
||||
|
||||
1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm
Symbolic link
1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/COH.DMC.aip.water.2dm
|
||||
@ -4,26 +4,26 @@ boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm COH.DMC.aip.water.2dm C Ow Hw # C-H2O
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
@ -31,21 +31,21 @@ neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
@ -4,26 +4,26 @@ boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm/opt COH.DMC.aip.water.2dm C Ow Hw # C-H2O
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
@ -31,21 +31,21 @@ neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm/opt
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm/opt
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
@ -457,9 +457,9 @@ mass *4 ${wheel_mass}
|
||||
variable dx equal 1.0
|
||||
variable density equal 0.001184
|
||||
|
||||
neighbor 0.5 bin
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
comm_modify cutoff 3.0
|
||||
comm_modify cutoff 3.0
|
||||
|
||||
pair_style lj/cut 1.2
|
||||
pair_coeff * * 0.0 0.0
|
||||
@ -474,7 +474,7 @@ reset_timestep 0
|
||||
#variable node_force equal "v_total_force / 178"
|
||||
#fix drag all addforce 0.0 0.0 0.0
|
||||
|
||||
velocity all set 0.0 -7.5.0 0.0 units box
|
||||
velocity all set 0.0 -7.5 0.0 units box
|
||||
|
||||
# viscosity of air is 0.0001847
|
||||
|
||||
|
||||
@ -1,4 +1,6 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-653-ge4a654c7cd-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
#===========================================================================#
|
||||
# Toy car driving down a system with a floor and ceiling. #
|
||||
# #
|
||||
@ -12,6 +14,7 @@ units cgs
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style atomic
|
||||
processors * 1 *
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
# Set up the simulation box
|
||||
@ -36,7 +39,7 @@ region mybox block -48 48 -90 630 -9 ${zh}
|
||||
region mybox block -48 48 -90 630 -9 87
|
||||
create_box 14 mybox
|
||||
Created orthogonal box = (-48 -90 -9) to (48 630 87)
|
||||
1 by 4 by 1 MPI processor grid
|
||||
2 by 1 by 2 MPI processor grid
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
# Creating the regions and filling them with atoms assigned to surge_group
|
||||
@ -647,9 +650,9 @@ fix 2 all nve
|
||||
#restart 100000 ParticleRestart
|
||||
|
||||
run 100000
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.5255396
|
||||
ghost atom cutoff = 2.5255396
|
||||
@ -660,53 +663,53 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.245 | 5.007 | 7.291 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
5000 29877588 4.6948567e-06 0 3.6195804e-05 3.987621e-12
|
||||
10000 27827776 7.2619763e-06 0 3.6601737e-05 4.407525e-12
|
||||
15000 26336751 8.3045873e-06 0 3.6072311e-05 4.7591238e-12
|
||||
20000 25052655 8.3618019e-06 0 3.477566e-05 5.0138704e-12
|
||||
25000 23854604 8.149944e-06 0 3.3300657e-05 5.1772301e-12
|
||||
30000 21629039 8.0369285e-06 0 3.0841153e-05 5.3056994e-12
|
||||
35000 20550367 7.0527369e-06 0 2.8719681e-05 5.253199e-12
|
||||
40000 18310227 6.4085866e-06 0 2.5713675e-05 5.1263402e-12
|
||||
45000 16963286 5.9460113e-06 0 2.3830975e-05 5.0913287e-12
|
||||
50000 15639408 5.1326227e-06 0 2.1621777e-05 4.8649712e-12
|
||||
55000 14004560 4.550004e-06 0 1.9315483e-05 4.6920784e-12
|
||||
60000 12777371 3.941146e-06 0 1.7412759e-05 4.4574594e-12
|
||||
65000 10919170 3.3361501e-06 0 1.4848599e-05 4.1051819e-12
|
||||
70000 9469421.4 2.7031575e-06 0 1.2687087e-05 3.7302586e-12
|
||||
75000 7926062.4 2.054775e-06 0 1.0411489e-05 3.3099123e-12
|
||||
80000 6314071.7 1.5118865e-06 0 8.169025e-06 2.8050899e-12
|
||||
85000 4847441.7 1.0803078e-06 0 6.1911288e-06 2.3005982e-12
|
||||
90000 3260324.1 6.858841e-07 0 4.1233536e-06 1.7789287e-12
|
||||
95000 1724645.4 3.1351302e-07 0 2.1318647e-06 1.1211538e-12
|
||||
100000 218390.81 4.4631827e-08 0 2.7488861e-07 3.8685559e-13
|
||||
Loop time of 647.752 on 4 procs for 100000 steps with 5092 atoms
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.685 | 6.044 | 7.403 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
5000 29842261 4.7942025e-06 0 3.6257904e-05 3.9879238e-12
|
||||
10000 28098061 7.2385794e-06 0 3.6863311e-05 4.4347259e-12
|
||||
15000 26888635 8.1191579e-06 0 3.6468752e-05 4.7939026e-12
|
||||
20000 24887991 8.3385518e-06 0 3.4578799e-05 4.9862342e-12
|
||||
25000 23265144 8.3946029e-06 0 3.2923828e-05 5.1750035e-12
|
||||
30000 21711263 7.6172235e-06 0 3.0508139e-05 5.2324506e-12
|
||||
35000 20102910 7.2232838e-06 0 2.8418459e-05 5.2342282e-12
|
||||
40000 18634097 6.5402802e-06 0 2.6186836e-05 5.2128024e-12
|
||||
45000 17486541 5.6292406e-06 0 2.4065889e-05 5.0867315e-12
|
||||
50000 15741195 4.96711e-06 0 2.1563581e-05 4.8546007e-12
|
||||
55000 14195280 4.6806146e-06 0 1.9647177e-05 4.7201162e-12
|
||||
60000 12378448 3.8806954e-06 0 1.693171e-05 4.3985323e-12
|
||||
65000 10976639 3.3069428e-06 0 1.4879983e-05 4.1055737e-12
|
||||
70000 9434340 2.6574414e-06 0 1.2604384e-05 3.703813e-12
|
||||
75000 7827664.3 2.1262358e-06 0 1.0379206e-05 3.3234802e-12
|
||||
80000 6487719.3 1.6234085e-06 0 8.4636294e-06 2.878629e-12
|
||||
85000 4761145.2 1.1556952e-06 0 6.175531e-06 2.3647084e-12
|
||||
90000 3196900 6.7497651e-07 0 4.0455759e-06 1.7461024e-12
|
||||
95000 1711466.2 3.2662861e-07 0 2.1310851e-06 1.1318791e-12
|
||||
100000 217597.05 4.394432e-08 0 2.7336422e-07 3.7619707e-13
|
||||
Loop time of 131.294 on 4 procs for 100000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.036284 | 19.922 | 79.572 | 771.6 | 3.08
|
||||
Neigh | 10.175 | 17.392 | 38.739 | 295.5 | 2.69
|
||||
Comm | 0.97616 | 1.0979 | 1.2312 | 8.6 | 0.17
|
||||
Output | 0.0043794 | 0.098646 | 0.13021 | 17.3 | 0.02
|
||||
Modify | 1.2262 | 132.11 | 524.58 |1971.4 | 20.39
|
||||
Other | | 477.1 | | | 73.66
|
||||
Pair | 0.0045648 | 9.3721 | 18.946 | 306.0 | 7.14
|
||||
Neigh | 2.8643 | 5.951 | 9.063 | 125.7 | 4.53
|
||||
Comm | 0.3616 | 0.90559 | 1.7801 | 61.8 | 0.69
|
||||
Output | 0.00058742 | 0.013642 | 0.026668 | 11.2 | 0.01
|
||||
Modify | 0.17841 | 50.602 | 101.42 | 708.8 | 38.54
|
||||
Other | | 64.45 | | | 49.09
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19856 ave 79424 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 1273 ave 2549 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 247 ave 496 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 19929 ave 39908 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 79424
|
||||
Ave neighs/atom = 15.5978
|
||||
Neighbor list builds = 4946
|
||||
Total # of neighbors = 79716
|
||||
Ave neighs/atom = 15.655145
|
||||
Neighbor list builds = 4954
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
@ -743,114 +746,114 @@ fix 3 all langevin 100000.0 5000.0 100.0 5678
|
||||
fix 2 all nve
|
||||
|
||||
run 200000
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.418 | 5.179 | 7.463 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100000 218390.81 0 0 2.3025679e-07 2.3133759e-14
|
||||
105000 103860.18 6.708614e-08 0 1.7658943e-07 6.9220989e-13
|
||||
110000 97287.339 7.0116647e-08 0 1.7268996e-07 7.4104867e-13
|
||||
115000 92211.102 6.7456604e-08 0 1.6467788e-07 7.2196879e-13
|
||||
120000 91577.119 6.8360083e-08 0 1.6491292e-07 7.3664397e-13
|
||||
125000 89670.176 6.7876707e-08 0 1.6241899e-07 7.29547e-13
|
||||
130000 87135.819 6.6698539e-08 0 1.5856877e-07 7.296178e-13
|
||||
135000 84795.008 6.3054439e-08 0 1.5245667e-07 7.1371044e-13
|
||||
140000 81222.266 6.4732255e-08 0 1.5036763e-07 7.2429578e-13
|
||||
145000 78548.301 6.3633278e-08 0 1.464494e-07 7.1795316e-13
|
||||
150000 76597.034 6.3093645e-08 0 1.4385248e-07 7.1457515e-13
|
||||
155000 73820.896 6.0685032e-08 0 1.3851689e-07 7.1093329e-13
|
||||
160000 71360.569 6.2615029e-08 0 1.3785288e-07 7.2019292e-13
|
||||
165000 67879.165 5.9691015e-08 0 1.3125831e-07 7.0403501e-13
|
||||
170000 66641.482 5.9273104e-08 0 1.2953546e-07 7.0719355e-13
|
||||
175000 65623.831 6.011737e-08 0 1.2930679e-07 7.1498836e-13
|
||||
180000 63627.376 5.8380162e-08 0 1.2546465e-07 7.0457247e-13
|
||||
185000 60865.93 5.8039489e-08 0 1.2221249e-07 7.1190327e-13
|
||||
190000 57329.276 5.8432616e-08 0 1.188768e-07 7.1940596e-13
|
||||
195000 54829.503 5.6354458e-08 0 1.1416305e-07 7.0364147e-13
|
||||
200000 52720.064 5.4124289e-08 0 1.0970883e-07 6.935829e-13
|
||||
205000 50368.95 5.4872306e-08 0 1.0797799e-07 7.0426031e-13
|
||||
210000 47452.093 5.3729225e-08 0 1.0375956e-07 6.994635e-13
|
||||
215000 45119.016 5.4481066e-08 0 1.0205156e-07 7.1418206e-13
|
||||
220000 43023.929 5.2752651e-08 0 9.8114229e-08 6.9834508e-13
|
||||
225000 40153.742 5.1097395e-08 0 9.3432837e-08 6.9738856e-13
|
||||
230000 39369.117 5.0504151e-08 0 9.2012337e-08 6.894872e-13
|
||||
235000 36113.296 4.9984145e-08 0 8.8059609e-08 6.9525606e-13
|
||||
240000 33557.343 4.74199e-08 0 8.2800537e-08 6.782253e-13
|
||||
245000 31543.784 4.6897571e-08 0 8.0155245e-08 6.7496202e-13
|
||||
250000 29448.798 4.5972171e-08 0 7.702103e-08 6.6988749e-13
|
||||
255000 26258.805 4.522174e-08 0 7.2907283e-08 6.7773348e-13
|
||||
260000 24024.155 4.4693255e-08 0 7.002273e-08 6.7584518e-13
|
||||
265000 22118.293 4.3984189e-08 0 6.730425e-08 6.7927214e-13
|
||||
270000 20024.409 4.2544987e-08 0 6.3657396e-08 6.8136681e-13
|
||||
275000 17107.549 4.1072236e-08 0 5.9109301e-08 6.666371e-13
|
||||
280000 14749.603 4.0000425e-08 0 5.5551428e-08 6.613669e-13
|
||||
285000 12500.706 4.0279102e-08 0 5.3459018e-08 6.8142024e-13
|
||||
290000 10030.224 3.8370444e-08 0 4.8945647e-08 6.7352743e-13
|
||||
295000 7601.7068 3.723413e-08 0 4.5248866e-08 6.6989317e-13
|
||||
300000 5231.1956 3.5917594e-08 0 4.143302e-08 6.6679331e-13
|
||||
Loop time of 1070.02 on 4 procs for 200000 steps with 5092 atoms
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.966 | 6.325 | 7.684 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100000 217597.05 0 0 2.294199e-07 2.3049678e-14
|
||||
105000 105542.67 6.5899047e-08 0 1.7717623e-07 6.9064382e-13
|
||||
110000 96801.947 6.6329049e-08 0 1.683906e-07 7.0960381e-13
|
||||
115000 93283.767 6.4052852e-08 0 1.6240507e-07 7.0033324e-13
|
||||
120000 90930.59 6.3799892e-08 0 1.5967108e-07 7.0244972e-13
|
||||
125000 90114.178 6.3511381e-08 0 1.5852179e-07 7.1128852e-13
|
||||
130000 83917.505 6.279089e-08 0 1.5126794e-07 6.9980391e-13
|
||||
135000 84057.326 6.269189e-08 0 1.5131636e-07 7.1046329e-13
|
||||
140000 80989.747 6.2166941e-08 0 1.4755716e-07 7.0822238e-13
|
||||
145000 79082.787 5.999291e-08 0 1.4337256e-07 7.0169908e-13
|
||||
150000 76377.704 6.0983734e-08 0 1.4151132e-07 7.0803269e-13
|
||||
155000 74642.465 5.8016291e-08 0 1.3671435e-07 6.8979034e-13
|
||||
160000 71320.499 5.8203836e-08 0 1.3339944e-07 6.9671842e-13
|
||||
165000 69769.632 5.8523021e-08 0 1.3208349e-07 6.9774909e-13
|
||||
170000 67002.509 5.6265118e-08 0 1.2690812e-07 6.8640935e-13
|
||||
175000 65045.732 5.5231406e-08 0 1.2381131e-07 6.8623008e-13
|
||||
180000 62633.05 5.3858988e-08 0 1.1989512e-07 6.7679278e-13
|
||||
185000 60510.328 5.3138189e-08 0 1.1693627e-07 6.7838603e-13
|
||||
190000 56958.939 5.3092173e-08 0 1.131459e-07 6.7336019e-13
|
||||
195000 55591.155 5.1736031e-08 0 1.1034766e-07 6.6906721e-13
|
||||
200000 53009.069 5.0934685e-08 0 1.0682393e-07 6.7160648e-13
|
||||
205000 50806.268 5.1266492e-08 0 1.0483325e-07 6.7042981e-13
|
||||
210000 47438.734 4.9024426e-08 0 9.9040681e-08 6.6234011e-13
|
||||
215000 45998.084 4.7751227e-08 0 9.6248556e-08 6.5536559e-13
|
||||
220000 43057.946 4.7441717e-08 0 9.2839159e-08 6.6414744e-13
|
||||
225000 41339.318 4.6636471e-08 0 9.0221906e-08 6.5621184e-13
|
||||
230000 37991.695 4.5885529e-08 0 8.5941452e-08 6.5311348e-13
|
||||
235000 36765.626 4.4005371e-08 0 8.2768609e-08 6.4411688e-13
|
||||
240000 33633.564 4.3031845e-08 0 7.8492844e-08 6.411006e-13
|
||||
245000 31441.462 4.186446e-08 0 7.5014252e-08 6.3558893e-13
|
||||
250000 28346.474 4.1330305e-08 0 7.1216947e-08 6.3547167e-13
|
||||
255000 26485.436 4.0303887e-08 0 6.8228374e-08 6.3491378e-13
|
||||
260000 24251.816 3.8404659e-08 0 6.3974165e-08 6.2184492e-13
|
||||
265000 21588.99 3.8470221e-08 0 6.1232221e-08 6.3046737e-13
|
||||
270000 19476.088 3.7190768e-08 0 5.7725063e-08 6.2042977e-13
|
||||
275000 17402.215 3.719862e-08 0 5.5546362e-08 6.3332028e-13
|
||||
280000 14911.078 3.5602533e-08 0 5.1323785e-08 6.2734446e-13
|
||||
285000 12478.751 3.4819713e-08 0 4.7976481e-08 6.2920228e-13
|
||||
290000 10052.548 3.3720905e-08 0 4.4319645e-08 6.2607642e-13
|
||||
295000 7653.5468 3.190337e-08 0 3.9972762e-08 6.210325e-13
|
||||
300000 5240.5437 3.0902841e-08 0 3.6428123e-08 6.2021355e-13
|
||||
Loop time of 240.576 on 4 procs for 200000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.057981 | 36.178 | 144.53 |1040.0 | 3.38
|
||||
Neigh | 0.25871 | 0.37261 | 0.69124 | 30.2 | 0.03
|
||||
Comm | 0.47965 | 0.49514 | 0.51697 | 2.1 | 0.05
|
||||
Output | 0.0064233 | 0.16356 | 0.21598 | 22.4 | 0.02
|
||||
Modify | 0.21709 | 229.82 | 918.61 |2623.2 | 21.48
|
||||
Other | | 803 | | | 75.04
|
||||
Pair | 0.0094455 | 19.351 | 39.054 | 439.7 | 8.04
|
||||
Neigh | 0.069968 | 0.11626 | 0.16266 | 13.6 | 0.05
|
||||
Comm | 0.10053 | 0.88025 | 1.9201 | 85.4 | 0.37
|
||||
Output | 0.0012827 | 0.02596 | 0.050595 | 15.3 | 0.01
|
||||
Modify | 0.03084 | 98.954 | 197.96 | 994.4 | 41.13
|
||||
Other | | 121.2 | | | 50.40
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19214.5 ave 76858 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 1273 ave 2547 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 175 ave 360 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 19108 ave 38228 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 76858
|
||||
Ave neighs/atom = 15.093873
|
||||
Neighbor list builds = 116
|
||||
Total # of neighbors = 76432
|
||||
Ave neighs/atom = 15.010212
|
||||
Neighbor list builds = 114
|
||||
Dangerous builds = 0
|
||||
|
||||
minimize 0.0 1.0e-8 1000 100000
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.418 | 5.461 | 8.588 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300000 5231.1956 3.5917594e-08 0 4.143302e-08 6.6679331e-13
|
||||
301000 5231.1956 3.591074e-08 0 4.1426165e-08 6.6674716e-13
|
||||
Loop time of 5.73822 on 4 procs for 1000 steps with 5092 atoms
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.966 | 6.887 | 8.809 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300000 5240.5437 3.0902841e-08 0 3.6428123e-08 6.2021355e-13
|
||||
301000 5240.5437 3.0896022e-08 0 3.6421304e-08 6.2016488e-13
|
||||
Loop time of 1.30229 on 4 procs for 1000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
3.59175937800124e-08 3.59107465269502e-08 3.59107396814365e-08
|
||||
Force two-norm initial, final = 8.3566626e-08 8.3465615e-08
|
||||
Force max component initial, final = 3.1363101e-09 3.1301201e-09
|
||||
Final line search alpha, max atom move = 1 3.1301201e-09
|
||||
3.09028409031651e-08 3.08960287166428e-08 3.08960219060082e-08
|
||||
Force two-norm initial, final = 8.2667468e-08 8.2568929e-08
|
||||
Force max component initial, final = 2.9188021e-09 2.9146337e-09
|
||||
Final line search alpha, max atom move = 1 2.9146337e-09
|
||||
Iterations, force evaluations = 1000 1000
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0003564 | 0.3119 | 1.2465 | 96.6 | 5.44
|
||||
Pair | 5.6358e-05 | 0.14395 | 0.28791 | 37.9 | 11.05
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0007532 | 0.00080708 | 0.000957 | 0.0 | 0.01
|
||||
Output | 4.88e-05 | 6.4775e-05 | 0.0001121 | 0.0 | 0.00
|
||||
Modify | 0.0004412 | 1.0758 | 4.3017 | 179.6 | 18.75
|
||||
Other | | 4.35 | | | 75.80
|
||||
Comm | 0.00010928 | 0.0035209 | 0.0074675 | 5.8 | 0.27
|
||||
Output | 1.9357e-05 | 2.0372e-05 | 2.2403e-05 | 0.0 | 0.00
|
||||
Modify | 4.6032e-05 | 0.4419 | 0.88539 | 66.5 | 33.93
|
||||
Other | | 0.7129 | | | 54.74
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19216 ave 76864 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 1273 ave 2547 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 175 ave 360 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 19105.5 ave 38227 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 76864
|
||||
Ave neighs/atom = 15.095051
|
||||
Total # of neighbors = 76422
|
||||
Ave neighs/atom = 15.008248
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
@ -884,22 +887,25 @@ pair_style lj/cut 1.2
|
||||
pair_coeff * * 0.0 0.0
|
||||
|
||||
timestep 0.025
|
||||
if "$(is_defined(dump,mydump))" then "undump mydump"
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
#dump mydump all atom 10000 run.lammpstrj
|
||||
#variable total_force equal 0.2
|
||||
#variable node_force equal "v_total_force / 178"
|
||||
#fix drag all addforce 0.0 0.0 0.0
|
||||
|
||||
velocity all set 0.0 -7.5.0 0.0 units box
|
||||
velocity all set 0.0 -7.5 0.0 units box
|
||||
|
||||
# viscosity of air is 0.0001847
|
||||
|
||||
fix FL all lb/fluid 1 0.0002 ${density} stencil 2 dx ${dx} zwall_velocity 0 0 # dumpxdmf 1000 sflow 0
|
||||
fix FL all lb/fluid 1 0.0002 0.001184 stencil 2 dx ${dx} zwall_velocity 0 0
|
||||
fix FL all lb/fluid 1 0.0002 0.001184 stencil 2 dx 1 zwall_velocity 0 0
|
||||
Using a lattice-Boltzmann grid of 96 by 720 by 97 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
Using a lattice-Boltzmann grid of 96 by 720 by 97 points.
|
||||
Local Grid Geometry created.
|
||||
First Run initialized
|
||||
|
||||
variable vx equal vcm(all,x)
|
||||
variable vy equal vcm(all,y)
|
||||
@ -925,11 +931,11 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
- fix lb/fluid command: doi:10.1016/j.cpc.2022.108318
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
author = {C. Denniston and N. Afrasiabian and M. G. Cole-Andre, F. E. Mackay and S. T. T. Ollila and T. Whitehead},
|
||||
title = {{LAMMPS} lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into {LAMMPS} Through a Lattice-{B}oltzmann Fluid}, journal = {Comput.\ Phys.\ Commun.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
@ -937,9 +943,9 @@ Your simulation uses code contributions which should be cited:
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.7
|
||||
ghost atom cutoff = 3
|
||||
@ -950,85 +956,15 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.03 | 14.01 | 16.94 Mbytes
|
||||
Step v_number_all v_node_mass f_FL[2] f_5[1] f_5[2] f_5[3]
|
||||
0 5092 98.193244 265447.33 0 0 0
|
||||
100 5092 98.193244 265447.33 -0.62398934 11.636864 -1.4385266
|
||||
200 5092 98.193244 265447.33 -0.0067390379 12.774129 0.77152356
|
||||
300 5092 98.193244 265447.33 -0.016866727 11.816838 0.164604
|
||||
400 5092 98.193244 265447.33 -0.099751559 14.292633 3.5403419
|
||||
500 5092 98.193244 265447.33 0.020826826 12.371064 3.4680188
|
||||
600 5092 98.193244 265447.33 -0.12187023 10.702747 0.7831029
|
||||
700 5092 98.193244 265447.33 -0.075493864 10.829418 0.98211649
|
||||
800 5092 98.193244 265447.33 -0.11468917 12.399304 1.7926202
|
||||
900 5092 98.193244 265447.33 -0.068927619 11.055182 2.4723876
|
||||
1000 5092 98.193244 265447.33 -0.069248548 10.39473 1.5087726
|
||||
1100 5092 98.193244 265447.33 0.065523336 9.4891653 1.3947719
|
||||
1200 5092 98.193244 265447.33 -0.044004235 11.847192 2.5397604
|
||||
1300 5092 98.193244 265447.33 0.040137088 10.997654 2.8832378
|
||||
1400 5092 98.193244 265447.33 0.067812628 10.154351 3.4014094
|
||||
1500 5092 98.193244 265447.33 0.026101525 10.034855 2.5467227
|
||||
1600 5092 98.193244 265447.33 0.023101669 11.834913 2.9961902
|
||||
1700 5092 98.193244 265447.33 -0.016678555 11.057297 1.1303356
|
||||
1800 5092 98.193244 265447.33 0.038804941 9.2005261 3.2383612
|
||||
1900 5092 98.193244 265447.33 0.045475707 8.592855 2.7327399
|
||||
2000 5092 98.193244 265447.33 0.0029052791 11.37239 1.650534
|
||||
2100 5092 98.193244 265447.33 0.0021721335 10.534175 1.4627128
|
||||
2200 5092 98.193244 265447.33 0.033545767 9.6499738 1.7555886
|
||||
2300 5092 98.193244 265447.33 0.037477935 10.604272 2.6811451
|
||||
2400 5092 98.193244 265447.33 0.013734867 9.5032009 3.4535601
|
||||
2500 5092 98.193244 265447.33 -0.074779755 10.655833 2.4798429
|
||||
2600 5092 98.193244 265447.33 -0.03912509 9.9731913 1.3805939
|
||||
2700 5092 98.193244 265447.33 0.084748343 9.6155874 1.9680204
|
||||
2800 5092 98.193244 265447.33 0.004716293 11.060178 2.3097572
|
||||
2900 5092 98.193244 265447.33 -0.01716838 10.851167 1.2315357
|
||||
3000 5092 98.193244 265447.33 0.0089978545 10.101686 1.6655875
|
||||
3100 5092 98.193244 265447.33 0.10214007 9.8489205 1.3991661
|
||||
3200 5092 98.193244 265447.33 0.030416619 10.303674 2.8620249
|
||||
3300 5092 98.193244 265447.33 -0.080891033 10.665193 1.6805084
|
||||
3400 5092 98.193244 265447.33 0.011781712 10.916621 0.79341262
|
||||
3500 5092 98.193244 265447.33 0.050815855 9.5573732 0.40493186
|
||||
3600 5092 98.193244 265447.33 -0.017225395 10.438887 2.303509
|
||||
3700 5092 98.193244 265447.33 0.0042521202 9.8119963 3.1057822
|
||||
3800 5092 98.193244 265447.33 0.037295562 9.3673981 2.2084367
|
||||
3900 5092 98.193244 265447.33 0.053448378 8.9799381 1.9075618
|
||||
4000 5092 98.193244 265447.33 0.039518888 10.999985 2.2441035
|
||||
4100 5092 98.193244 265447.33 -0.022548252 10.07084 1.7986935
|
||||
4200 5092 98.193244 265447.33 0.093070808 8.8837865 1.8491384
|
||||
4300 5092 98.193244 265447.33 0.16605392 10.080625 2.3851261
|
||||
4400 5092 98.193244 265447.33 0.071707012 11.041363 1.3512251
|
||||
4500 5092 98.193244 265447.33 -0.044985642 10.590977 0.89464128
|
||||
4600 5092 98.193244 265447.33 0.010801743 9.745945 1.3254718
|
||||
4700 5092 98.193244 265447.33 0.11301693 9.8629299 1.2450238
|
||||
4800 5092 98.193244 265447.33 0.29083508 10.35163 1.6481913
|
||||
4900 5092 98.193244 265447.33 0.274316 9.7650593 1.6979411
|
||||
5000 5092 98.193244 265447.33 -0.041118665 9.9508487 1.7688687
|
||||
Loop time of 5880.47 on 4 procs for 5000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.8823 | 1.2112 | 1.6656 | 29.1 | 0.02
|
||||
Neigh | 22.261 | 23.161 | 24.045 | 15.0 | 0.39
|
||||
Comm | 1.1838 | 1.3636 | 1.6084 | 14.2 | 0.02
|
||||
Output | 0.99304 | 0.99848 | 1.0061 | 0.5 | 0.02
|
||||
Modify | 5850 | 5851.7 | 5853.1 | 1.6 | 99.51
|
||||
Other | | 2.046 | | | 0.03
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8835 ave 35340 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 35340
|
||||
Ave neighs/atom = 6.9402985
|
||||
Neighbor list builds = 2500
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
Total wall time: 2:06:45
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.67 | 16.66 | 18.64 Mbytes
|
||||
Step v_number_all v_node_mass f_FL[2] f_5[1] f_5[2] f_5[3]
|
||||
0 5092 98.193244 265447.33 0 0 0
|
||||
100 5092 98.193244 265447.33 0.42848502 10.910894 -2.3324154
|
||||
200 5092 98.193244 265447.33 -0.02627078 13.323497 0.5134388
|
||||
300 5092 98.193244 265447.33 0.33955198 12.017917 0.07308431
|
||||
400 5092 98.193244 265447.33 0.28511704 14.563626 3.4626969
|
||||
500 5092 98.193244 265447.33 -0.080267505 11.795121 3.266271
|
||||
600 5092 98.193244 265447.33 0.11024837 10.763593 0.68027763
|
||||
700 5092 98.193244 265447.33 0.22058041 10.773118 1.1020572
|
||||
800 5092 98.193244 265447.33 0.26569373 12.841207 1.7015156
|
||||
900 5092
|
||||
@ -5,7 +5,7 @@
|
||||
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
|
||||
project(paceplugin VERSION 1.0 LANGUAGES CXX)
|
||||
project(paceplugin VERSION 1.1 LANGUAGES CXX)
|
||||
|
||||
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
|
||||
include(CheckIncludeFileCXX)
|
||||
@ -15,7 +15,11 @@ include(ML-PACE)
|
||||
##########################
|
||||
# building the plugins
|
||||
|
||||
add_library(paceplugin MODULE paceplugin.cpp ${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace.cpp)
|
||||
add_library(paceplugin MODULE paceplugin.cpp
|
||||
${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace.cpp
|
||||
${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace_extrapolation.cpp
|
||||
${LAMMPS_SOURCE_DIR}/ML-PACE/compute_pace.cpp)
|
||||
|
||||
target_link_libraries(paceplugin PRIVATE pace)
|
||||
target_link_libraries(paceplugin PRIVATE lammps)
|
||||
target_include_directories(paceplugin PRIVATE ${LAMMPS_SOURCE_DIR}/ML-PACE)
|
||||
|
||||
@ -3,6 +3,8 @@
|
||||
#include "version.h"
|
||||
|
||||
#include "pair_pace.h"
|
||||
#include "pair_pace_extrapolation.h"
|
||||
#include "compute_pace.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -11,6 +13,16 @@ static Pair *pair_pace_creator(LAMMPS *lmp)
|
||||
return new PairPACE(lmp);
|
||||
}
|
||||
|
||||
static Pair *pair_pace_extrapolation_creator(LAMMPS *lmp)
|
||||
{
|
||||
return new PairPACEExtrapolation(lmp);
|
||||
}
|
||||
|
||||
static Compute *compute_pace_creator(LAMMPS *lmp, int argc, char **argv)
|
||||
{
|
||||
return new ComputePACE(lmp, argc, argv);
|
||||
}
|
||||
|
||||
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
|
||||
{
|
||||
lammpsplugin_t plugin;
|
||||
@ -25,4 +37,24 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
|
||||
plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_pace_creator;
|
||||
plugin.handle = handle;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
|
||||
// register pace/extrapolation pair style
|
||||
plugin.version = LAMMPS_VERSION;
|
||||
plugin.style = "pair";
|
||||
plugin.name = "pace/extrapolation";
|
||||
plugin.info = "PACE plugin extrapolation pair style v1.0";
|
||||
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
|
||||
plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_pace_extrapolation_creator;
|
||||
plugin.handle = handle;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
|
||||
// register pace compute style
|
||||
plugin.version = LAMMPS_VERSION;
|
||||
plugin.style = "compute";
|
||||
plugin.name = "pace";
|
||||
plugin.info = "PACE plugin compute style v1.0";
|
||||
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
|
||||
plugin.creator.v2 = (lammpsplugin_factory2 *) &compute_pace_creator;
|
||||
plugin.handle = handle;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
}
|
||||
|
||||
@ -39,7 +39,7 @@ InstallDir "$LOCALAPPDATA\${PACEPLUGIN}"
|
||||
|
||||
ShowInstDetails show
|
||||
ShowUninstDetails show
|
||||
SetCompressor lzma
|
||||
SetCompressor zlib
|
||||
|
||||
!define MUI_ABORTWARNING
|
||||
|
||||
|
||||
1
examples/PACKAGES/pafi/Fe_mm.eam.fs
Symbolic link
1
examples/PACKAGES/pafi/Fe_mm.eam.fs
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/Fe_mm.eam.fs
|
||||
59
examples/PACKAGES/plumed/plugin/CMakeLists.txt
Normal file
59
examples/PACKAGES/plumed/plugin/CMakeLists.txt
Normal file
@ -0,0 +1,59 @@
|
||||
# -*- CMake -*- build system for plugin examples.
|
||||
# The is meant to be used as a template for plugins that are
|
||||
# distributed independent from the LAMMPS package.
|
||||
##########################################
|
||||
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
|
||||
project(plumedplugin VERSION 1.0 LANGUAGES CXX)
|
||||
|
||||
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
|
||||
include(CheckIncludeFileCXX)
|
||||
include(LAMMPSInterfacePlugin)
|
||||
include(PLUMED)
|
||||
|
||||
##########################
|
||||
# building the plugins
|
||||
|
||||
add_library(plumedplugin MODULE plumedplugin.cpp ${LAMMPS_SOURCE_DIR}/PLUMED/fix_plumed.cpp)
|
||||
target_link_libraries(plumedplugin PRIVATE LAMMPS::PLUMED)
|
||||
target_link_libraries(plumedplugin PRIVATE lammps)
|
||||
target_include_directories(plumedplugin PRIVATE ${LAMMPS_SOURCE_DIR}/PLUMED)
|
||||
set_target_properties(plumedplugin PROPERTIES PREFIX "" SUFFIX ".so")
|
||||
|
||||
# MacOS seems to need this
|
||||
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
|
||||
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
|
||||
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
|
||||
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
|
||||
set_target_properties(plumedplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
|
||||
if(CMAKE_CROSSCOMPILING)
|
||||
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
|
||||
endif()
|
||||
|
||||
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
|
||||
find_program(MAKENSIS_PATH makensis)
|
||||
if(MAKENSIS_PATH)
|
||||
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico
|
||||
${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/plumedplugin.nsis
|
||||
${CMAKE_BINARY_DIR})
|
||||
if(BUILD_MPI)
|
||||
if(USE_MSMPI)
|
||||
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MSMPI plumedplugin.nsis
|
||||
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
|
||||
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MSMPI.exe)
|
||||
else()
|
||||
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI plumedplugin.nsis
|
||||
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
|
||||
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MPI.exe)
|
||||
endif()
|
||||
else()
|
||||
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} plumedplugin.nsis
|
||||
COMMAND ${CMAKE_COMMAND} -E echo ${PWD}
|
||||
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
|
||||
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}.exe)
|
||||
endif()
|
||||
endif()
|
||||
else()
|
||||
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-rdynamic")
|
||||
endif()
|
||||
1
examples/PACKAGES/plumed/plugin/LAMMPSInterfacePlugin.cmake
Symbolic link
1
examples/PACKAGES/plumed/plugin/LAMMPSInterfacePlugin.cmake
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../cmake/Modules/LAMMPSInterfacePlugin.cmake
|
||||
1
examples/PACKAGES/plumed/plugin/PLUMED.cmake
Symbolic link
1
examples/PACKAGES/plumed/plugin/PLUMED.cmake
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../cmake/Modules/Packages/PLUMED.cmake
|
||||
2
examples/PACKAGES/plumed/plugin/README.txt
Normal file
2
examples/PACKAGES/plumed/plugin/README.txt
Normal file
@ -0,0 +1,2 @@
|
||||
This folder contains a loader and support files to build the PLUMED package as plugin.
|
||||
For more information please see: https://docs.lammps.org/Developer_plugins.html
|
||||
BIN
examples/PACKAGES/plumed/plugin/lammps-text-logo-wide.bmp
Normal file
BIN
examples/PACKAGES/plumed/plugin/lammps-text-logo-wide.bmp
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 25 KiB |
BIN
examples/PACKAGES/plumed/plugin/lammps.ico
Normal file
BIN
examples/PACKAGES/plumed/plugin/lammps.ico
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 204 KiB |
28
examples/PACKAGES/plumed/plugin/plumedplugin.cpp
Normal file
28
examples/PACKAGES/plumed/plugin/plumedplugin.cpp
Normal file
@ -0,0 +1,28 @@
|
||||
|
||||
#include "lammpsplugin.h"
|
||||
#include "version.h"
|
||||
|
||||
#include "fix_plumed.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
static Fix *fix_plumed_creator(LAMMPS *lmp, int argc, char **argv)
|
||||
{
|
||||
return new FixPlumed(lmp, argc, argv);
|
||||
}
|
||||
|
||||
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
|
||||
{
|
||||
lammpsplugin_t plugin;
|
||||
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
|
||||
|
||||
// register plumed fix style
|
||||
plugin.version = LAMMPS_VERSION;
|
||||
plugin.style = "fix";
|
||||
plugin.name = "plumed";
|
||||
plugin.info = "Plumed2 plugin fix style v1.0";
|
||||
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
|
||||
plugin.creator.v1 = (lammpsplugin_factory1 *) &fix_plumed_creator;
|
||||
plugin.handle = handle;
|
||||
(*register_plugin)(&plugin, lmp);
|
||||
}
|
||||
172
examples/PACKAGES/plumed/plugin/plumedplugin.nsis
Normal file
172
examples/PACKAGES/plumed/plugin/plumedplugin.nsis
Normal file
@ -0,0 +1,172 @@
|
||||
#!Nsis Installer Command Script
|
||||
#
|
||||
# The following external defines are recognized:
|
||||
# ${VERSION} = YYYYMMDD
|
||||
|
||||
!include "MUI2.nsh"
|
||||
!include "FileFunc.nsh"
|
||||
|
||||
!define MUI_ICON "lammps.ico"
|
||||
!define MUI_UNICON "lammps.ico"
|
||||
!define MUI_HEADERIMAGE
|
||||
!define MUI_HEADERIMAGE_BITMAP "lammps-text-logo-wide.bmp"
|
||||
!define MUI_HEADERIMAGE_RIGHT
|
||||
|
||||
Unicode true
|
||||
XPStyle on
|
||||
|
||||
!include "LogicLib.nsh"
|
||||
!addplugindir "envvar/Plugins/x86-unicode"
|
||||
!include "x64.nsh"
|
||||
|
||||
RequestExecutionLevel user
|
||||
|
||||
!macro VerifyUserIsAdmin
|
||||
UserInfo::GetAccountType
|
||||
pop $0
|
||||
${If} $0 != "admin"
|
||||
messageBox mb_iconstop "Administrator rights required!"
|
||||
setErrorLevel 740 ;ERROR_ELEVATION_REQUIRED
|
||||
quit
|
||||
${EndIf}
|
||||
!macroend
|
||||
|
||||
!define PLUMEDPLUGIN "LAMMPS PLUMED Plugin ${VERSION}"
|
||||
OutFile "LAMMPS-PLUMED-plugin-${VERSION}.exe"
|
||||
|
||||
Name "${PLUMEDPLUGIN}"
|
||||
InstallDir "$LOCALAPPDATA\${PLUMEDPLUGIN}"
|
||||
|
||||
ShowInstDetails show
|
||||
ShowUninstDetails show
|
||||
SetCompressor zlib
|
||||
|
||||
!define MUI_ABORTWARNING
|
||||
|
||||
!insertmacro MUI_PAGE_DIRECTORY
|
||||
!insertmacro MUI_PAGE_INSTFILES
|
||||
|
||||
!insertmacro MUI_UNPAGE_CONFIRM
|
||||
!insertmacro MUI_UNPAGE_INSTFILES
|
||||
|
||||
!insertmacro MUI_LANGUAGE "English"
|
||||
|
||||
function .onInit
|
||||
# Determine if LAMMPS was already installed and check whether it was in 32-bit
|
||||
# or 64-bit. Then look up path to uninstaller and offer to uninstall or quit
|
||||
SetRegView 32
|
||||
ReadRegDWORD $0 HKCU "Software\LAMMPS-PLUMED" "Bits"
|
||||
SetRegView LastUsed
|
||||
${If} $0 == "32"
|
||||
SetRegView 32
|
||||
${ElseIf} $0 == "64"
|
||||
SetRegView 64
|
||||
${Else}
|
||||
SetRegView 64
|
||||
${EndIf}
|
||||
ClearErrors
|
||||
ReadRegStr $R0 HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" "UninstallString"
|
||||
SetRegView LastUsed
|
||||
${If} ${Errors}
|
||||
DetailPrint "LAMMPS PLUMED plugin not (yet) installed"
|
||||
${Else}
|
||||
MessageBox MB_YESNO "LAMMPS PLUMED plugin ($0 bit) is already installed. Uninstall existing version?" /SD IDYES IDNO Quit
|
||||
Pop $R1
|
||||
StrCmp $R1 2 Quit +1
|
||||
Exec $R0
|
||||
Quit:
|
||||
Quit
|
||||
${EndIf}
|
||||
setShellVarContext all
|
||||
functionEnd
|
||||
|
||||
Section "${PLUMEDPLUGIN}" SecPlumedplugin
|
||||
SectionIn RO
|
||||
# Write LAMMPS installation bitness marker. Always use 32-bit registry view
|
||||
SetRegView 32
|
||||
IntFmt $0 "0x%08X" 64
|
||||
WriteRegDWORD HKCU "Software\LAMMPS-PLUMED" "Bits" $0
|
||||
|
||||
# Switch to "native" registry view
|
||||
SetRegView 64
|
||||
SetShellVarContext current
|
||||
|
||||
SetOutPath "$INSTDIR"
|
||||
CreateDirectory "$INSTDIR\patches"
|
||||
CreateDirectory "$INSTDIR\bin"
|
||||
File lammps.ico
|
||||
File plumedplugin.so
|
||||
|
||||
SetOutPath "$INSTDIR\bin"
|
||||
File plumed.exe
|
||||
|
||||
# Register Application and its uninstaller
|
||||
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
|
||||
"DisplayName" "${PLUMEDPLUGIN}"
|
||||
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
|
||||
"Publisher" "The LAMMPS and PLUMED Developers"
|
||||
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
|
||||
"URLInfoAbout" "lammps.org"
|
||||
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
|
||||
"DisplayIcon" "$INSTDIR\lammps.ico"
|
||||
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
|
||||
"DisplayVersion" "${VERSION}"
|
||||
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
|
||||
"InstallLocation" "$INSTDIR"
|
||||
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
|
||||
"UninstallString" "$\"$INSTDIR\uninstall.exe$\""
|
||||
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
|
||||
"QuietUninstallString" "$\"$INSTDIR\uninstall.exe$\" /S"
|
||||
|
||||
${GetSize} "$INSTDIR" "/S=0K" $0 $1 $2
|
||||
IntFmt $0 "0x%08X" $0
|
||||
WriteRegDWORD HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
|
||||
"EstimatedSize" "$0"
|
||||
|
||||
# update path variables
|
||||
EnVar::SetHKCU
|
||||
# add plumed executable path
|
||||
EnVar::AddValue "PATH" "$INSTDIR\bin"
|
||||
# add to LAMMPS plugin search path
|
||||
EnVar::AddValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
|
||||
# add plumed2 patch files
|
||||
EnVar::AddValue "PLUMED_ROOT" "$INSTDIR"
|
||||
|
||||
WriteUninstaller "$INSTDIR\Uninstall.exe"
|
||||
SectionEnd
|
||||
|
||||
function un.onInit
|
||||
SetShellVarContext current
|
||||
functionEnd
|
||||
|
||||
Section "Uninstall"
|
||||
# remove LAMMPS bitness/installation indicator always in 32-bit registry view
|
||||
SetRegView 32
|
||||
DeleteRegKey HKCU "Software\LAMMPS-PLUMED"
|
||||
|
||||
# unregister extension, and uninstall info
|
||||
SetRegView 64
|
||||
SetShellVarContext current
|
||||
# unregister installation
|
||||
DeleteRegKey HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED"
|
||||
|
||||
# update path variables
|
||||
EnVar::SetHKCU
|
||||
# remove plumed executable path
|
||||
EnVar::DeleteValue "PATH" "$INSTDIR\bin"
|
||||
# remove entry from LAMMPS plugin search path
|
||||
EnVar::DeleteValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
|
||||
# remove plumed patch environment
|
||||
EnVar::Delete "PLUMED_ROOT"
|
||||
|
||||
RMDir /r /REBOOTOK "$INSTDIR\patches"
|
||||
RMDir /r /REBOOTOK "$INSTDIR\bin"
|
||||
Delete /REBOOTOK "$INSTDIR\plumedplugin.so"
|
||||
Delete /REBOOTOK "$INSTDIR\Uninstall.exe"
|
||||
Delete /REBOOTOK "$INSTDIR\lammps.ico"
|
||||
RMDir /REBOOTOK "$INSTDIR"
|
||||
SectionEnd
|
||||
|
||||
# Local Variables:
|
||||
# mode: sh
|
||||
# End:
|
||||
@ -44,6 +44,7 @@ thermo 50
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
|
||||
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
|
||||
|
||||
fix 1 statted_grp_REACT nvt temp 300 300 100
|
||||
|
||||
|
||||
@ -47,7 +47,7 @@ thermo 50
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 &
|
||||
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
|
||||
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 rescale_charges yes
|
||||
|
||||
fix 1 statted_grp_REACT nvt temp 300 300 100
|
||||
|
||||
|
||||
@ -44,7 +44,7 @@ thermo 50
|
||||
|
||||
fix myrxns all bond/react stabilization no &
|
||||
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
|
||||
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
|
||||
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
|
||||
|
||||
fix 1 all nve/limit .03
|
||||
|
||||
|
||||
@ -48,27 +48,6 @@ Types
|
||||
17 hc
|
||||
18 hc
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
16 0.000000
|
||||
17 0.000000
|
||||
18 0.000000
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
|
||||
@ -44,21 +44,21 @@ Types
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.410000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 -0.820000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.410000
|
||||
1 -0.60533
|
||||
2 -0.01149
|
||||
3 -0.76306
|
||||
4 0.38
|
||||
5 0.29346
|
||||
6 0.18360
|
||||
7 0.15396
|
||||
8 -0.72636
|
||||
9 -0.27437
|
||||
10 0.40603
|
||||
11 -0.65530
|
||||
12 -0.76
|
||||
13 0.21423
|
||||
14 0.18949
|
||||
15 0.38
|
||||
|
||||
Molecules
|
||||
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
1
examples/PACKAGES/ti/Cu_mishin1.eam.alloy
Symbolic link
1
examples/PACKAGES/ti/Cu_mishin1.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/Cu_mishin1.eam.alloy
|
||||
@ -1,219 +0,0 @@
|
||||
LAMMPS (4 May 2022)
|
||||
units lj
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style bpm/sphere
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block -25 15 -22 22 -22 22
|
||||
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
|
||||
create_atoms 1 region disk
|
||||
Created 7529 atoms
|
||||
using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
group plate region disk
|
||||
7529 atoms in group plate
|
||||
|
||||
region ball sphere 8.0 0.0 0.0 6.0
|
||||
create_atoms 1 region ball
|
||||
Created 3589 atoms
|
||||
using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
group projectile region ball
|
||||
3589 atoms in group projectile
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 134598738
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 1.0 bin
|
||||
pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1
|
||||
pair_coeff 1 1
|
||||
|
||||
fix 1 all nve/bpm/sphere
|
||||
|
||||
create_bonds many plate plate 1 0.0 1.5
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 1, bins = 64 70 70
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair gran/hooke/history, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Added 38559 bonds, new total = 38559
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
15 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
create_bonds many projectile projectile 2 0.0 1.5
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Bonds are defined but no bond style is set (../force.cpp:192)
|
||||
WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:194)
|
||||
Added 21869 bonds, new total = 60428
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
16 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/rotational store/local brkbond 100 time id1 id2
|
||||
bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.2 0.002 0.002
|
||||
bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.2 0.002 0.002
|
||||
|
||||
velocity projectile set -0.05 0.0 0.0
|
||||
compute nbond all nbond/atom
|
||||
compute tbond all reduce sum c_nbond
|
||||
|
||||
timestep 0.05
|
||||
thermo_style custom step ke pe pxx pyy pzz c_tbond
|
||||
thermo 100
|
||||
thermo_modify lost ignore lost/bond ignore
|
||||
#dump 1 all custom 100 atomDump id radius x y z c_nbond
|
||||
|
||||
dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
|
||||
dump_modify 2 header no
|
||||
|
||||
run 7500
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 0.65, bins = 98 108 108
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gran/hooke/history, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 33.22 | 33.22 | 33.22 Mbytes
|
||||
Step KinEng PotEng Pxx Pyy Pzz c_tbond
|
||||
0 0.00053238861 0 3.8217307e-05 -7.6534847e-14 1.9906102e-13 10.8703
|
||||
100 0.00053238861 0 3.8217307e-05 -4.2831948e-13 5.7428612e-13 10.8703
|
||||
200 0.00053238861 0 3.8217307e-05 -1.4067913e-12 1.4975493e-12 10.8703
|
||||
300 0.00053238861 0 3.8217307e-05 -8.77782e-13 3.8245851e-13 10.8703
|
||||
400 0.00053238861 0 3.8217307e-05 -8.5835238e-13 6.5448014e-13 10.8703
|
||||
500 0.00053093549 0 4.0340893e-05 4.501394e-07 5.3690512e-07 10.8703
|
||||
600 0.00051485902 0 6.6761034e-05 4.6258948e-06 5.2285428e-06 10.869221
|
||||
700 0.00049942978 0 9.5499005e-05 9.3031413e-07 4.5389354e-06 10.85501
|
||||
800 0.00049465262 0 5.6810167e-05 -5.5619903e-06 -1.6010295e-06 10.820651
|
||||
900 0.00048784775 0 1.5747004e-05 2.0522042e-05 2.5481542e-05 10.769563
|
||||
1000 0.00048345699 0 2.1159666e-05 1.2232747e-05 1.4767665e-05 10.730347
|
||||
1100 0.00047945073 0 5.2779833e-05 -2.6136504e-05 -2.7689007e-05 10.703184
|
||||
1200 0.00047512604 0 6.3234312e-05 -1.7082136e-05 -2.9178979e-05 10.686634
|
||||
1300 0.00047401428 0 2.5474717e-05 -7.4782876e-06 -1.9808965e-05 10.678
|
||||
1400 0.00047619121 0 2.5189461e-05 2.9476227e-06 -4.4149511e-06 10.671704
|
||||
1500 0.0004668728 0 5.8798861e-05 -2.6192143e-06 1.0805172e-06 10.666127
|
||||
1600 0.00045088371 0 5.8377694e-05 2.2911269e-06 4.339717e-06 10.66073
|
||||
1700 0.00044275099 0 4.0766018e-05 2.7748031e-05 2.8202527e-05 10.6458
|
||||
1800 0.0004424362 0 3.0460351e-05 2.9690484e-05 3.3464889e-05 10.620615
|
||||
1900 0.00043678957 0 3.809598e-05 2.4448755e-06 1.2651201e-05 10.603166
|
||||
2000 0.00042747562 0 4.2315209e-05 -7.6783024e-06 -3.3357359e-06 10.576003
|
||||
2100 0.0004214344 0 2.6171505e-05 5.5424035e-06 -4.1153085e-06 10.539845
|
||||
2200 0.00041712779 0 3.0796803e-05 1.1362383e-05 7.7103875e-07 10.49937
|
||||
2300 0.00041095769 0 4.141148e-05 1.4142023e-06 -1.0982633e-05 10.471668
|
||||
2400 0.00040883568 0 3.5835323e-05 -1.0216635e-05 -2.3669763e-05 10.45116
|
||||
2500 0.00040762685 0 2.879385e-05 -1.4074395e-05 -1.9314875e-05 10.437309
|
||||
2600 0.00040579873 0 2.771644e-05 -2.316844e-05 -2.2961097e-05 10.422378
|
||||
2700 0.00040340975 0 3.4482945e-05 -3.075929e-05 -2.3321344e-05 10.410505
|
||||
2800 0.00040170914 0 3.1147943e-05 -2.4329639e-05 -1.1787678e-05 10.400792
|
||||
2900 0.00040015113 0 2.3214992e-05 -1.8068374e-05 3.8127871e-06 10.393416
|
||||
3000 0.00040029253 0 2.7275906e-05 -7.0762689e-06 1.3782424e-05 10.385321
|
||||
3100 0.00040037329 0 2.962113e-05 -1.3795312e-06 5.3267315e-06 10.378485
|
||||
3200 0.00040142612 0 2.86096e-05 4.4289601e-06 -3.3950404e-06 10.373988
|
||||
3300 0.00040105092 0 2.5423615e-05 9.5689359e-06 -2.5296344e-06 10.370031
|
||||
3400 0.00039950673 0 2.6405258e-05 9.5776239e-06 -7.3789982e-07 10.364274
|
||||
3500 0.00039715236 0 3.115696e-05 1.0986224e-05 6.6898207e-06 10.360496
|
||||
3600 0.00039446552 0 2.8426837e-05 9.6296098e-06 1.5057875e-05 10.353121
|
||||
3700 0.00039263296 0 2.567768e-05 6.347291e-06 2.4842157e-05 10.346645
|
||||
3800 0.00039061341 0 2.7635193e-05 5.0165135e-06 2.5989901e-05 10.341069
|
||||
3900 0.00038985051 0 2.8639932e-05 1.056365e-05 2.4463803e-05 10.329196
|
||||
4000 0.00038815347 0 2.6613146e-05 2.0316396e-05 2.1434368e-05 10.318043
|
||||
4100 0.00038651302 0 2.4759493e-05 1.9632349e-05 1.3524912e-05 10.311027
|
||||
4200 0.00038565809 0 2.5290845e-05 1.9908233e-05 8.3895516e-06 10.299155
|
||||
4300 0.0003847255 0 2.6461182e-05 1.9385332e-05 5.664874e-06 10.292319
|
||||
4400 0.0003844421 0 2.4464435e-05 1.4675545e-05 6.8223863e-06 10.286203
|
||||
4500 0.0003842788 0 2.3080348e-05 7.1469159e-06 6.8395849e-06 10.278287
|
||||
4600 0.00038365139 0 2.4937615e-05 2.3854793e-06 4.6100509e-06 10.270732
|
||||
4700 0.00038271503 0 2.431281e-05 -3.127707e-06 3.8840673e-07 10.264796
|
||||
4800 0.00038233688 0 2.3727372e-05 -3.9575833e-06 1.5658614e-06 10.25742
|
||||
4900 0.00038223496 0 2.3842519e-05 2.6005447e-06 4.5031882e-06 10.246987
|
||||
5000 0.00038219402 0 2.4705111e-05 8.2018492e-06 4.0121467e-06 10.240511
|
||||
5100 0.00038195153 0 2.5112089e-05 9.1687723e-06 3.3825795e-06 10.236014
|
||||
5200 0.00038170903 0 2.4166312e-05 4.6680528e-06 3.0359762e-06 10.232236
|
||||
5300 0.00038194303 0 2.4293657e-05 3.067111e-06 2.1353614e-06 10.230617
|
||||
5400 0.00038147407 0 2.472142e-05 5.2915485e-06 -1.7472423e-06 10.230098
|
||||
5500 0.00038156894 0 2.4839317e-05 6.6216457e-06 -2.7544087e-06 10.227759
|
||||
5600 0.00038169434 0 2.4600407e-05 3.8679618e-06 1.2622251e-07 10.2256
|
||||
5700 0.00038219734 0 2.4459589e-05 2.0025919e-07 -1.1917672e-08 10.223621
|
||||
5800 0.00038268758 0 2.4768428e-05 8.7913744e-07 -1.4000329e-06 10.222902
|
||||
5900 0.00038300658 0 2.4827866e-05 3.6621944e-06 -2.2178729e-07 10.222182
|
||||
6000 0.00038250316 0 2.4309432e-05 4.3755483e-06 2.2736019e-06 10.221123
|
||||
6100 0.0003821526 0 2.4396115e-05 3.3855804e-06 4.4742551e-06 10.219503
|
||||
6200 0.00038185711 0 2.4795348e-05 1.7569948e-06 4.3229904e-06 10.219503
|
||||
6300 0.00038197679 0 2.4817115e-05 1.237731e-07 3.9285574e-06 10.218604
|
||||
6400 0.00038232311 0 2.4723664e-05 -8.7946112e-07 2.6215619e-06 10.217884
|
||||
6500 0.00038255543 0 2.4821878e-05 -4.8948257e-07 3.9392146e-07 10.217704
|
||||
6600 0.00038251887 0 2.4923895e-05 -1.1107041e-07 -8.3900047e-07 10.217344
|
||||
6700 0.00038177389 0 2.4664007e-05 -6.4474733e-07 -2.1004826e-06 10.218084
|
||||
6800 0.00038096291 0 2.4262293e-05 -1.7159941e-06 -2.8149643e-06 10.218103
|
||||
6900 0.00038090601 0 2.4179172e-05 -2.2622259e-06 -2.1268271e-06 10.217024
|
||||
7000 0.00038088094 0 2.4363443e-05 -2.4652531e-06 -8.209416e-07 10.215944
|
||||
7100 0.00038094624 0 2.5119358e-05 -1.5432706e-06 1.1465135e-06 10.214684
|
||||
7200 0.00038168738 0 2.5565338e-05 -1.4052753e-07 3.3146851e-06 10.212705
|
||||
7300 0.00038200854 0 2.5436565e-05 4.353807e-07 3.3504276e-06 10.212345
|
||||
7400 0.00038187543 0 2.4764819e-05 6.7297502e-07 1.5923471e-06 10.213084
|
||||
7500 0.00038165297 0 2.4015684e-05 7.8657712e-07 1.0138435e-06 10.214742
|
||||
Loop time of 32.2292 on 4 procs for 7500 steps with 11111 atoms
|
||||
|
||||
Performance: 1005300.744 tau/day, 232.709 timesteps/s
|
||||
96.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.29763 | 0.30464 | 0.31393 | 1.1 | 0.95
|
||||
Bond | 25.936 | 26.533 | 27.431 | 11.7 | 82.33
|
||||
Neigh | 0.60911 | 0.63557 | 0.66475 | 2.8 | 1.97
|
||||
Comm | 1.7247 | 2.7138 | 3.3823 | 40.5 | 8.42
|
||||
Output | 0.020408 | 0.020935 | 0.02227 | 0.5 | 0.06
|
||||
Modify | 1.8299 | 1.8724 | 1.9325 | 2.9 | 5.81
|
||||
Other | | 0.1491 | | | 0.46
|
||||
|
||||
Nlocal: 2777.75 ave 2887 max 2682 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 1152.5 ave 1189 max 1125 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Neighs: 11515.5 ave 12520 max 10831 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 46062
|
||||
Ave neighs/atom = 4.1456215
|
||||
Ave special neighs/atom = 10.214742
|
||||
Neighbor list builds = 408
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:32
|
||||
340
examples/charmmfsw/charmmff.cmap
Normal file
340
examples/charmmfsw/charmmff.cmap
Normal file
@ -0,0 +1,340 @@
|
||||
#CMAP for C NH1 CT1 C NH1 CT1 C NH1; id=1
|
||||
#phi = -180.000000
|
||||
0.130000 0.770000 0.970000 1.250000 2.120000
|
||||
2.720000 2.090000 1.790000 0.780000 -0.690000
|
||||
1.000000 -2.200000 -4.830000 -4.820000 -4.910000
|
||||
-3.590000 -2.770000 -2.780000 -2.450000 -2.350000
|
||||
-2.340000 -1.520000 -0.950000 -0.040000
|
||||
|
||||
#phi = -165.000000
|
||||
-0.130000 1.380000 1.580000 1.870000 2.400000
|
||||
2.490000 2.440000 1.930000 1.090000 0.640000
|
||||
0.260000 -2.800000 -4.010000 -4.140000 -3.420000
|
||||
-2.600000 -2.300000 -1.500000 -1.100000 -0.860000
|
||||
-0.640000 -0.210000 -1.080000 -1.120000
|
||||
|
||||
#phi = -150.000000
|
||||
0.080000 1.420000 1.620000 2.050000 2.650000
|
||||
2.720000 2.320000 1.990000 1.560000 2.460000
|
||||
-0.230000 -1.820000 -2.580000 -3.010000 -2.550000
|
||||
-1.890000 -1.350000 -0.730000 0.070000 -0.230000
|
||||
-0.770000 -1.280000 -1.290000 -0.820000
|
||||
|
||||
#phi = -135.000000
|
||||
0.930000 1.520000 2.240000 2.550000 3.110000
|
||||
2.920000 2.460000 2.190000 2.060000 1.850000
|
||||
0.120000 -1.180000 -2.000000 -2.280000 -1.960000
|
||||
-1.340000 -0.930000 0.020000 0.310000 -0.520000
|
||||
-1.150000 -0.980000 -0.570000 -0.440000
|
||||
|
||||
#phi = -120.000000
|
||||
1.360000 1.960000 2.700000 3.040000 3.700000
|
||||
3.560000 2.640000 2.770000 2.720000 1.630000
|
||||
0.710000 -0.790000 -2.120000 -2.630000 -1.800000
|
||||
-0.430000 -0.060000 0.440000 0.910000 -0.550000
|
||||
-0.970000 -0.860000 -0.250000 0.450000
|
||||
|
||||
#phi = -105.000000
|
||||
2.050000 2.540000 2.820000 3.090000 3.370000
|
||||
3.550000 3.070000 2.900000 2.960000 2.120000
|
||||
0.910000 -0.820000 -2.090000 -2.240000 -1.460000
|
||||
0.210000 0.080000 0.770000 1.040000 -0.120000
|
||||
-0.320000 -0.160000 0.310000 0.730000
|
||||
|
||||
#phi = -90.000000
|
||||
1.450000 2.750000 2.740000 3.160000 3.450000
|
||||
3.340000 3.180000 3.900000 3.340000 2.440000
|
||||
0.910000 -0.610000 -1.510000 -1.620000 -0.960000
|
||||
-0.020000 0.420000 0.910000 0.460000 0.150000
|
||||
-0.070000 0.020000 0.280000 0.750000
|
||||
|
||||
#phi = -75.000000
|
||||
1.380000 3.350000 2.350000 3.060000 3.810000
|
||||
3.700000 3.580000 4.210000 3.540000 1.690000
|
||||
0.100000 -0.680000 -0.120000 -0.430000 -0.600000
|
||||
0.230000 0.420000 0.300000 0.550000 0.190000
|
||||
-0.250000 -0.190000 -0.250000 0.470000
|
||||
|
||||
#phi = -60.000000
|
||||
0.240000 1.230000 1.720000 3.170000 4.210000
|
||||
4.390000 4.280000 3.670000 2.270000 -0.480000
|
||||
-0.410000 -0.040000 -0.360000 -0.820000 -0.170000
|
||||
0.140000 0.270000 0.320000 0.310000 -0.670000
|
||||
-0.950000 -1.530000 -1.480000 -0.200000
|
||||
|
||||
#phi = -45.000000
|
||||
-1.180000 0.080000 2.350000 4.210000 5.380000
|
||||
5.390000 4.380000 2.460000 1.120000 0.110000
|
||||
0.010000 -0.150000 -0.800000 -0.580000 0.080000
|
||||
0.270000 -0.050000 0.380000 0.250000 -0.890000
|
||||
-1.580000 -1.950000 -1.980000 -2.000000
|
||||
|
||||
#phi = -30.000000
|
||||
-1.170000 1.070000 4.180000 6.740000 6.070000
|
||||
4.810000 2.780000 1.320000 0.770000 -0.010000
|
||||
0.280000 -0.710000 1.310000 1.520000 1.920000
|
||||
2.220000 0.190000 0.530000 0.330000 -1.600000
|
||||
-2.850000 -3.550000 -3.280000 -2.660000
|
||||
|
||||
#phi = -15.000000
|
||||
0.290000 5.590000 3.730000 3.220000 3.270000
|
||||
2.520000 1.590000 1.380000 0.860000 0.660000
|
||||
1.620000 0.850000 0.510000 0.740000 1.020000
|
||||
1.620000 -0.340000 0.180000 -0.610000 -2.560000
|
||||
-3.790000 -3.810000 -3.160000 -1.750000
|
||||
|
||||
#phi = 0.000000
|
||||
2.830000 0.790000 0.320000 0.480000 0.630000
|
||||
0.980000 1.240000 1.670000 1.650000 2.520000
|
||||
1.610000 0.780000 0.120000 0.070000 0.120000
|
||||
-1.570000 -1.210000 -1.930000 -2.600000 -3.790000
|
||||
-3.930000 -3.620000 -2.680000 -0.920000
|
||||
|
||||
#phi = 15.000000
|
||||
-0.780000 -1.910000 -2.050000 -1.850000 -1.050000
|
||||
0.180000 1.680000 2.220000 1.360000 2.450000
|
||||
1.440000 0.680000 -0.240000 -0.540000 -0.790000
|
||||
-2.180000 -3.210000 -4.350000 -3.940000 -3.910000
|
||||
-3.460000 -2.770000 1.760000 0.310000
|
||||
|
||||
#phi = 30.000000
|
||||
-2.960000 -3.480000 -3.440000 -2.400000 -1.130000
|
||||
0.340000 1.430000 1.390000 0.970000 2.460000
|
||||
1.520000 0.550000 -0.410000 -1.480000 -3.580000
|
||||
-4.130000 -4.560000 -4.440000 -3.580000 -2.960000
|
||||
-1.960000 -1.070000 -1.600000 -2.450000
|
||||
|
||||
#phi = 45.000000
|
||||
-4.020000 -3.840000 -3.370000 -2.330000 -0.980000
|
||||
0.360000 0.810000 0.750000 0.500000 1.900000
|
||||
0.770000 -0.420000 -3.290000 -3.910000 -4.520000
|
||||
-4.890000 -3.850000 -4.150000 -2.670000 -2.370000
|
||||
-2.860000 -3.420000 -3.670000 -3.600000
|
||||
|
||||
#phi = 60.000000
|
||||
-3.350000 -2.980000 -2.320000 -1.240000 -0.260000
|
||||
0.720000 0.670000 0.440000 2.400000 1.630000
|
||||
-2.010000 -3.310000 -3.990000 -4.530000 -4.850000
|
||||
-3.770000 -3.940000 -3.890000 -2.610000 -3.510000
|
||||
-3.760000 -3.640000 -3.450000 -3.340000
|
||||
|
||||
#phi = 75.000000
|
||||
-2.250000 -1.640000 -1.010000 0.040000 0.640000
|
||||
0.820000 0.520000 -0.010000 -0.370000 -1.190000
|
||||
-2.390000 -3.380000 -4.500000 -5.590000 -5.510000
|
||||
-4.940000 -3.830000 -3.840000 -3.700000 -4.150000
|
||||
-4.170000 -3.730000 -3.740000 -2.620000
|
||||
|
||||
#phi = 90.000000
|
||||
-1.720000 -1.180000 -0.430000 0.280000 0.810000
|
||||
0.800000 0.480000 -0.340000 -0.790000 -1.770000
|
||||
-2.810000 -3.800000 -5.220000 -6.280000 -6.580000
|
||||
-5.640000 -5.060000 -4.020000 -4.150000 -4.470000
|
||||
-4.100000 -3.770000 -3.160000 -2.650000
|
||||
|
||||
#phi = 105.000000
|
||||
-1.850000 -1.090000 -0.450000 0.130000 1.010000
|
||||
0.880000 0.490000 -0.220000 -0.860000 -1.680000
|
||||
-3.010000 -4.130000 -5.990000 -6.860000 -6.830000
|
||||
-5.850000 -3.860000 -4.860000 -4.910000 -4.720000
|
||||
-4.600000 -4.090000 -3.270000 -2.410000
|
||||
|
||||
#phi = 120.000000
|
||||
-1.970000 -1.120000 -0.540000 -0.150000 0.760000
|
||||
1.040000 0.760000 0.310000 -0.330000 -1.870000
|
||||
-3.370000 -5.010000 -6.120000 -7.050000 -6.980000
|
||||
-3.700000 -4.510000 -5.090000 -5.420000 -4.850000
|
||||
-4.440000 -4.000000 -3.420000 -2.750000
|
||||
|
||||
#phi = 135.000000
|
||||
-2.110000 -1.170000 -0.320000 -0.010000 0.320000
|
||||
1.090000 0.940000 0.630000 -0.170000 -1.830000
|
||||
-3.470000 -4.950000 -6.110000 -1.920000 -4.050000
|
||||
-5.000000 -5.000000 -4.840000 -4.890000 -4.300000
|
||||
-4.490000 -4.440000 -4.160000 -3.180000
|
||||
|
||||
#phi = 150.000000
|
||||
-1.760000 -0.400000 0.020000 0.360000 0.630000
|
||||
1.260000 1.360000 0.950000 -0.070000 -1.480000
|
||||
-3.150000 1.840000 -1.760000 -5.090000 -5.740000
|
||||
-5.390000 -4.780000 -4.190000 -4.120000 -4.040000
|
||||
-4.130000 -4.030000 -4.030000 -2.940000
|
||||
|
||||
#phi = 165.000000
|
||||
-0.810000 -0.070000 0.380000 0.540000 1.280000
|
||||
1.640000 1.700000 1.520000 0.630000 -1.090000
|
||||
-2.740000 -0.740000 -4.560000 -6.410000 -5.890000
|
||||
-5.140000 -4.190000 -3.670000 -3.840000 -3.560000
|
||||
-3.550000 -3.250000 -2.750000 -1.810000
|
||||
|
||||
|
||||
#CMAP for C NH1 CT2 C NH1 CT2 C NH1; id=2
|
||||
#phi = -180.000000
|
||||
0.235350 0.182300 0.177200 0.396800 0.859400
|
||||
1.489700 2.092500 2.297700 1.808600 0.696200
|
||||
-0.563300 -1.432700 -1.015100 1.426300 -0.564300
|
||||
0.696200 1.808200 2.301700 2.092600 1.489100
|
||||
0.859500 0.396900 0.176900 0.182400
|
||||
|
||||
#phi = -165.000000
|
||||
0.020100 -0.203800 -0.269700 0.014200 0.620800
|
||||
1.392400 2.046200 2.188200 1.683900 0.688500
|
||||
-0.373700 -0.703500 0.837800 3.704000 -0.730100
|
||||
0.594100 1.713100 2.205800 2.026400 1.529800
|
||||
1.027400 0.623800 0.348400 0.182800
|
||||
|
||||
#phi = -150.000000
|
||||
-0.533600 -0.807400 -0.804600 -0.379800 0.365300
|
||||
1.168000 1.641000 1.618100 1.302200 0.615100
|
||||
0.065700 0.738500 2.959500 -2.036600 -0.934600
|
||||
0.407900 1.517000 1.984800 1.833100 1.435200
|
||||
0.995600 0.562200 0.150600 -0.209000
|
||||
|
||||
#phi = -135.000000
|
||||
-1.208500 -1.429400 -1.319200 -0.817500 -0.112400
|
||||
0.454400 0.737600 0.879300 0.850100 0.670300
|
||||
0.943500 -2.651200 -2.829400 -2.199100 -1.065700
|
||||
0.279600 1.322000 1.668300 1.521300 1.193900
|
||||
0.765300 0.246000 -0.315500 -0.823200
|
||||
|
||||
#phi = -120.000000
|
||||
-1.789100 -1.965500 -1.860700 -1.447900 -0.896500
|
||||
-0.401000 -0.015100 0.321300 0.634600 0.976300
|
||||
-1.977500 -2.883200 -2.848500 -2.137900 -0.960300
|
||||
0.308700 1.098100 1.245300 1.133600 0.881800
|
||||
0.448200 -0.153900 -0.823700 -1.404300
|
||||
|
||||
#phi = -105.000000
|
||||
-2.246700 -2.487000 -2.473700 -2.135600 -1.577700
|
||||
-0.980600 -0.429100 0.144700 0.734000 -0.918300
|
||||
-2.299200 -2.882200 -2.668600 -1.847100 -0.719800
|
||||
0.107000 0.496000 0.553500 0.584300 0.494000
|
||||
0.098300 -0.529800 -1.237900 -1.840100
|
||||
|
||||
#phi = -90.000000
|
||||
-2.851100 -3.181100 -3.199500 -2.785300 -2.054300
|
||||
-1.242900 -0.476500 0.288100 -0.045300 -1.470600
|
||||
-2.558800 -2.869400 -2.450300 -1.582200 -0.930800
|
||||
-0.426400 -0.022700 0.000000 -0.097400 -0.136100
|
||||
-0.439600 -1.038600 -1.741000 -2.373200
|
||||
|
||||
#phi = -75.000000
|
||||
-3.961800 -4.268200 -4.109000 -3.364700 -2.252200
|
||||
-1.140400 -0.209800 0.487300 -0.746200 -2.127700
|
||||
-2.932100 -2.898500 -2.247900 -1.730400 -1.177200
|
||||
-0.448200 0.034900 -0.073300 -0.531600 -0.933300
|
||||
-1.360700 -2.009200 -2.745700 -3.424900
|
||||
|
||||
#phi = -60.000000
|
||||
-5.408000 -5.355100 -4.640100 -3.283200 -1.710200
|
||||
-0.423800 0.354400 -0.103700 -1.577700 -2.828300
|
||||
-3.151200 -2.649200 -2.183000 -1.761200 -0.981700
|
||||
-0.174700 0.262600 0.039200 -0.663000 -1.530700
|
||||
-2.478200 -3.465600 -4.334200 -5.011200
|
||||
|
||||
#phi = -45.000000
|
||||
-6.093200 -5.298400 -3.816620 -1.922530 -0.196160
|
||||
0.768200 0.568500 -0.831300 -2.343900 -3.037100
|
||||
-2.663700 -2.191100 -2.022900 -1.438500 -0.649000
|
||||
0.077000 0.441500 0.257500 -0.491100 -1.820600
|
||||
-3.473100 -4.895200 -5.790700 -6.205900
|
||||
|
||||
#phi = -30.000000
|
||||
-5.258225 -3.675795 -1.631110 0.430085 1.496470
|
||||
0.318200 -0.555100 -1.695500 -2.434200 -2.192600
|
||||
-1.691300 -1.890000 -1.708500 -1.206300 -0.567400
|
||||
0.054300 0.497200 0.599600 -0.171000 -2.137600
|
||||
-4.237000 -5.584100 -6.135100 -6.067000
|
||||
|
||||
#phi = -15.000000
|
||||
-3.161820 -0.902080 1.432450 -1.452885 -1.560780
|
||||
-1.665600 -1.783100 -1.755100 -1.329300 -0.731100
|
||||
-1.317000 -1.662800 -1.601200 -1.294900 -0.817300
|
||||
-0.197100 0.549500 0.850400 -0.689700 -2.819900
|
||||
-4.393000 -5.111500 -5.205690 -4.654785
|
||||
|
||||
#phi = 0.000000
|
||||
0.034035 -2.349860 -3.412065 -3.620070 -3.450950
|
||||
-2.875650 -1.787800 -0.541250 0.410450 -0.372500
|
||||
-1.126850 -1.498450 -1.608700 -1.498450 -1.126850
|
||||
-0.372500 0.410450 -0.541250 -1.787800 -2.875650
|
||||
-3.450950 -3.620070 -3.412065 -2.349860
|
||||
|
||||
#phi = 15.000000
|
||||
-3.162345 -4.654785 -5.205690 -5.111500 -4.393000
|
||||
-2.819900 -0.689700 0.850400 0.549500 -0.197100
|
||||
-0.817300 -1.294900 -1.601200 -1.662800 -1.317000
|
||||
-0.731100 -1.329300 -1.755100 -1.783100 -1.665600
|
||||
-1.560780 -1.452885 1.432450 -0.902080
|
||||
|
||||
#phi = 30.000000
|
||||
-5.258220 -6.067000 -6.135100 -5.584100 -4.237000
|
||||
-2.137600 -0.171000 0.599600 0.497200 0.054300
|
||||
-0.567400 -1.206300 -1.708500 -1.890000 -1.691300
|
||||
-2.192600 -2.434200 -1.695500 -0.555100 0.318200
|
||||
1.496470 0.430085 -1.631110 -3.675795
|
||||
|
||||
#phi = 45.000000
|
||||
-6.093300 -6.205900 -5.790700 -4.895200 -3.473100
|
||||
-1.820600 -0.491100 0.257500 0.441500 0.077000
|
||||
-0.649000 -1.438500 -2.022900 -2.191100 -2.663700
|
||||
-3.037100 -2.343900 -0.831300 0.568500 0.768200
|
||||
-0.196160 -1.922530 -3.816620 -5.298400
|
||||
|
||||
#phi = 60.000000
|
||||
-5.407500 -5.011200 -4.334200 -3.465600 -2.478200
|
||||
-1.530700 -0.663000 0.039200 0.262600 -0.174700
|
||||
-0.981700 -1.761200 -2.183000 -2.649200 -3.151200
|
||||
-2.828300 -1.577700 -0.103700 0.354400 -0.423800
|
||||
-1.710200 -3.283200 -4.640100 -5.355100
|
||||
|
||||
#phi = 75.000000
|
||||
-3.961900 -3.424900 -2.745700 -2.009200 -1.360700
|
||||
-0.933300 -0.531600 -0.073300 0.034900 -0.448200
|
||||
-1.177200 -1.730400 -2.247900 -2.898500 -2.932100
|
||||
-2.127700 -0.746200 0.487300 -0.209800 -1.140400
|
||||
-2.252200 -3.364700 -4.109000 -4.268200
|
||||
|
||||
#phi = 90.000000
|
||||
-2.854500 -2.373200 -1.741000 -1.038600 -0.439600
|
||||
-0.136100 -0.097400 0.000000 -0.022700 -0.426400
|
||||
-0.930800 -1.582200 -2.450300 -2.869400 -2.558800
|
||||
-1.470600 -0.045300 0.288100 -0.476500 -1.242900
|
||||
-2.054300 -2.785300 -3.199500 -3.181100
|
||||
|
||||
#phi = 105.000000
|
||||
-2.246400 -1.840100 -1.237900 -0.529800 0.098300
|
||||
0.494000 0.584300 0.553500 0.496000 0.107000
|
||||
-0.719800 -1.847100 -2.668600 -2.882200 -2.299200
|
||||
-0.918300 0.734000 0.144700 -0.429100 -0.980600
|
||||
-1.577700 -2.135600 -2.473700 -2.487000
|
||||
|
||||
#phi = 120.000000
|
||||
-1.788800 -1.404300 -0.823700 -0.153900 0.448200
|
||||
0.881800 1.133600 1.245300 1.098100 0.308700
|
||||
-0.960300 -2.137900 -2.848500 -2.883200 -1.977500
|
||||
0.976300 0.634600 0.321300 -0.015100 -0.401000
|
||||
-0.896500 -1.447900 -1.860700 -1.965500
|
||||
|
||||
#phi = 135.000000
|
||||
-1.208900 -0.823200 -0.315500 0.246000 0.765300
|
||||
1.193900 1.521300 1.668300 1.322000 0.279600
|
||||
-1.065700 -2.199100 -2.829400 -2.651200 0.943500
|
||||
0.670300 0.850100 0.879300 0.737600 0.454400
|
||||
-0.112400 -0.817500 -1.319200 -1.429400
|
||||
|
||||
#phi = 150.000000
|
||||
-0.533400 -0.209000 0.150600 0.562200 0.995600
|
||||
1.435200 1.833100 1.984800 1.517000 0.407900
|
||||
-0.934600 -2.036600 2.959500 0.738500 0.065700
|
||||
0.615100 1.302200 1.618100 1.641000 1.168000
|
||||
0.365300 -0.379800 -0.804600 -0.807400
|
||||
|
||||
#phi = 165.000000
|
||||
0.019900 0.182800 0.348400 0.623800 1.027400
|
||||
1.529800 2.026400 2.205800 1.713100 0.594100
|
||||
-0.730100 3.704000 0.837800 -0.703500 -0.373700
|
||||
0.688500 1.683900 2.188200 2.046200 1.392400
|
||||
0.620800 0.014200 -0.269700 -0.203800
|
||||
|
||||
|
||||
BIN
examples/charmmfsw/data.charmmfsw.gz
Normal file
BIN
examples/charmmfsw/data.charmmfsw.gz
Normal file
Binary file not shown.
46
examples/charmmfsw/in.charmmfsw
Normal file
46
examples/charmmfsw/in.charmmfsw
Normal file
@ -0,0 +1,46 @@
|
||||
# charmmfsw example generated by https://charmm-gui.org/
|
||||
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
|
||||
#
|
||||
# Dependencies: packages MOLECULE / KSPACE / RIGID
|
||||
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
newton off
|
||||
pair_style lj/charmmfsw/coul/long 10 12
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-6
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmmfsw
|
||||
special_bonds charmm
|
||||
improper_style harmonic
|
||||
timestep 2
|
||||
|
||||
fix cmap all cmap charmmff.cmap
|
||||
fix_modify cmap energy yes
|
||||
read_data data.charmmfsw.gz fix cmap crossterm CMAP
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
fix 1 all shake 1e-6 100 100 m 1.008 a 142
|
||||
fix 2 all nvt temp 303.15 303.15 100.0
|
||||
|
||||
# for visualization with LAMMPS-GUI
|
||||
group water type 18 60
|
||||
group nowater subtract all water
|
||||
group ions type 63 64
|
||||
group other subtract all water ions
|
||||
|
||||
# dump viz other image 10 myimage-*.ppm element type size 800 800 zoom 2.82954 shiny 0.5 fsaa yes bond none none view 20 10 box no 0.0 axes no 0.0 0.0 center s 0.521318 0.489856 0.489856
|
||||
# dump_modify viz pad 9 boxcolor darkblue backcolor darkgray element H H H H H H H H H H H H H H H H H H C C C C C C C C C C C C C C C C C C C N N N N N N N N N N N N N N O O O O O O O O O P S Cl K adiam 1 1.92 adiam 2 1.92 adiam 3 1.92 adiam 4 1.92 adiam 5 1.92 adiam 6 1.92 adiam 7 1.92 adiam 8 1.92 adiam 9 1.92 adiam 10 1.92 adiam 11 1.92 adiam 12 1.92 adiam 13 1.92 adiam 14 1.92 adiam 15 1.92 adiam 16 1.92 adiam 17 1.92 adiam 18 1.92 adiam 19 2.72 adiam 20 2.72 adiam 21 2.72 adiam 22 2.72 adiam 23 2.72 adiam 24 2.72 adiam 25 2.72 adiam 26 2.72 adiam 27 2.72 adiam 28 2.72 adiam 29 2.72 adiam 30 2.72 adiam 31 2.72 adiam 32 2.72 adiam 33 2.72 adiam 34 2.72 adiam 35 2.72 adiam 36 2.72 adiam 37 2.72 adiam 38 2.48 adiam 39 2.48 adiam 40 2.48 adiam 41 2.48 adiam 42 2.48 adiam 43 2.48 adiam 44 2.48 adiam 45 2.48 adiam 46 2.48 adiam 47 2.48 adiam 48 2.48 adiam 49 2.48 adiam 50 2.48 adiam 51 2.48 adiam 52 2.432 adiam 53 2.432 adiam 54 2.432 adiam 55 2.432 adiam 56 2.432 adiam 57 2.432 adiam 58 2.432 adiam 59 2.432 adiam 60 2.432 adiam 61 2.88 adiam 62 2.88 adiam 63 3.632 adiam 64 2.816
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
|
||||
|
||||
run 100
|
||||
|
||||
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.1
Normal file
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.1
Normal file
@ -0,0 +1,221 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# charmmfsw example generated by https://charmm-gui.org/
|
||||
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
|
||||
#
|
||||
# Dependencies: packages MOLECULE / KSPACE / RIGID
|
||||
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
newton off
|
||||
pair_style lj/charmmfsw/coul/long 10 12
|
||||
Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:63)
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-6
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmmfsw
|
||||
special_bonds charmm
|
||||
improper_style harmonic
|
||||
timestep 2
|
||||
|
||||
fix cmap all cmap charmmff.cmap
|
||||
Reading CMAP parameters from: charmmff.cmap
|
||||
Read in CMAP data for 2 crossterm types
|
||||
fix_modify cmap energy yes
|
||||
read_data data.charmmfsw.gz fix cmap crossterm CMAP
|
||||
Reading data file ...
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10245 atoms
|
||||
reading velocities ...
|
||||
10245 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
15 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
48 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
6973 bonds
|
||||
reading angles ...
|
||||
4057 angles
|
||||
reading dihedrals ...
|
||||
1363 dihedrals
|
||||
reading impropers ...
|
||||
70 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
|
||||
9 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.072 seconds
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
fix 1 all shake 1e-6 100 100 m 1.008 a 142
|
||||
Finding SHAKE clusters ...
|
||||
75 = # of size 2 clusters
|
||||
47 = # of size 3 clusters
|
||||
9 = # of size 4 clusters
|
||||
3265 = # of frozen angles
|
||||
find clusters CPU = 0.003 seconds
|
||||
fix 2 all nvt temp 303.15 303.15 100.0
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.27938162
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00036407395
|
||||
estimated relative force accuracy = 1.0963718e-06
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 226981 157464
|
||||
Generated 2016 of 2016 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 2 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmmfsw/coul/long, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 16 1.09 1.38032e-07 6
|
||||
Bond: 18 1.09 1.00046e-07 3
|
||||
Bond: 34 1.111 1.11388e-06 10
|
||||
Bond: 39 1.111 4.83041e-08 5
|
||||
Bond: 43 1.111 1.97842e-07 10
|
||||
Bond: 44 1.111 1.71815e-06 10
|
||||
Bond: 59 1.111 8.42509e-08 2
|
||||
Bond: 62 1.111 2.84854e-08 2
|
||||
Bond: 63 1.111 2.14153e-07 46
|
||||
Bond: 64 1.111 1.59305e-07 18
|
||||
Bond: 65 1.08 5.67061e-07 16
|
||||
Bond: 66 1.08 1.43965e-06 4
|
||||
Bond: 67 1 1.81926e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 1.34571e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 2.71955e-07 6530
|
||||
Bond: 75 1 1.46045e-07 10
|
||||
Bond: 79 0.997 5.24499e-07 17
|
||||
Bond: 81 1 1.32984e-07 4
|
||||
Bond: 84 1.04 7.65389e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 5.75241e-07 2
|
||||
Bond: 97 1.325 4.3613e-08 3
|
||||
Angle: 142 104.52 2.67611e-05 3265
|
||||
Per MPI rank memory allocation (min/avg/max) = 143.6 | 143.6 | 143.6 Mbytes
|
||||
Step TotEng E_vdwl E_coul E_long E_dihed PotEng KinEng Temp Press
|
||||
0 -27877.652 3447.5013 144035.68 -182420.51 343.05623 -34213.5 6335.8474 307.44113 -989.27065
|
||||
10 -27879.086 3334.4154 144205.4 -182416.19 348.14696 -34133.566 6254.4808 303.49289 -1211.2863
|
||||
20 -27882.193 3293.7931 144272.04 -182415.87 333.20456 -34116.91 6234.7164 302.53384 -1041.5231
|
||||
30 -27886.779 3177.7183 144344.61 -182409.28 340.77044 -34166.241 6279.462 304.70508 -1538.0247
|
||||
40 -27892.698 3186.4294 144409.85 -182417.01 337.80177 -34097.62 6204.9214 301.08807 -1516.1201
|
||||
50 -27898.215 3198.5531 144426.3 -182405.24 336.58074 -34049.909 6151.6947 298.50529 -1349.4431
|
||||
60 -27900.589 3163.4592 144400.32 -182414.85 341.17705 -34110.926 6210.3369 301.35085 -1695.3697
|
||||
70 -27900.487 3223.7183 144242.71 -182409.21 341.09496 -34188.493 6288.0059 305.11967 -1493.2031
|
||||
80 -27901.07 3274.244 144265.07 -182417.68 344.0409 -34177.343 6276.2725 304.55032 -1273.0263
|
||||
90 -27905.672 3237.6056 144288.71 -182418.22 342.15013 -34187.814 6282.1417 304.83511 -1268.0436
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 16 1.09 3.78281e-07 6
|
||||
Bond: 18 1.09 1.12288e-07 3
|
||||
Bond: 34 1.111 7.60709e-07 10
|
||||
Bond: 39 1.111 2.37855e-07 5
|
||||
Bond: 43 1.111 6.00872e-07 10
|
||||
Bond: 44 1.111 3.75324e-07 10
|
||||
Bond: 59 1.111 1.12311e-07 2
|
||||
Bond: 62 1.111 2.99471e-07 2
|
||||
Bond: 63 1.111 6.10589e-07 46
|
||||
Bond: 64 1.111 4.50733e-07 18
|
||||
Bond: 65 1.08 2.90668e-07 16
|
||||
Bond: 66 1.08 1.61592e-07 4
|
||||
Bond: 67 1 5.4508e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 4.1398e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 1.76706e-06 6530
|
||||
Bond: 75 1 3.96686e-07 10
|
||||
Bond: 79 0.997 7.72922e-07 17
|
||||
Bond: 81 1 1.30673e-07 4
|
||||
Bond: 84 1.04 1.44551e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 1.03526e-07 2
|
||||
Bond: 97 1.325 3.64689e-08 3
|
||||
Angle: 142 104.52 0.000130126 3265
|
||||
100 -27913.241 3159.0677 144299.1 -182414.94 336.48839 -34254.412 6341.1706 307.69943 -1421.2905
|
||||
Loop time of 11.5304 on 1 procs for 100 steps with 10245 atoms
|
||||
|
||||
Performance: 1.499 ns/day, 16.014 hours/ns, 8.673 timesteps/s, 88.852 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.6772 | 8.6772 | 8.6772 | 0.0 | 75.25
|
||||
Bond | 0.012444 | 0.012444 | 0.012444 | 0.0 | 0.11
|
||||
Kspace | 1.2286 | 1.2286 | 1.2286 | 0.0 | 10.66
|
||||
Neigh | 1.5276 | 1.5276 | 1.5276 | 0.0 | 13.25
|
||||
Comm | 0.010441 | 0.010441 | 0.010441 | 0.0 | 0.09
|
||||
Output | 0.00055001 | 0.00055001 | 0.00055001 | 0.0 | 0.00
|
||||
Modify | 0.07101 | 0.07101 | 0.07101 | 0.0 | 0.62
|
||||
Other | | 0.002628 | | | 0.02
|
||||
|
||||
Nlocal: 10245 ave 10245 max 10245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 30479 ave 30479 max 30479 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7.05928e+06 ave 7.05928e+06 max 7.05928e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7059275
|
||||
Ave neighs/atom = 689.04588
|
||||
Ave special neighs/atom = 2.3664226
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:11
|
||||
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.4
Normal file
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.4
Normal file
@ -0,0 +1,221 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# charmmfsw example generated by https://charmm-gui.org/
|
||||
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
|
||||
#
|
||||
# Dependencies: packages MOLECULE / KSPACE / RIGID
|
||||
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
newton off
|
||||
pair_style lj/charmmfsw/coul/long 10 12
|
||||
Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:63)
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-6
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmmfsw
|
||||
special_bonds charmm
|
||||
improper_style harmonic
|
||||
timestep 2
|
||||
|
||||
fix cmap all cmap charmmff.cmap
|
||||
Reading CMAP parameters from: charmmff.cmap
|
||||
Read in CMAP data for 2 crossterm types
|
||||
fix_modify cmap energy yes
|
||||
read_data data.charmmfsw.gz fix cmap crossterm CMAP
|
||||
Reading data file ...
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10245 atoms
|
||||
reading velocities ...
|
||||
10245 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
15 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
48 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
6973 bonds
|
||||
reading angles ...
|
||||
4057 angles
|
||||
reading dihedrals ...
|
||||
1363 dihedrals
|
||||
reading impropers ...
|
||||
70 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
|
||||
9 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.068 seconds
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
fix 1 all shake 1e-6 100 100 m 1.008 a 142
|
||||
Finding SHAKE clusters ...
|
||||
75 = # of size 2 clusters
|
||||
47 = # of size 3 clusters
|
||||
9 = # of size 4 clusters
|
||||
3265 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
fix 2 all nvt temp 303.15 303.15 100.0
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.27938162
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00036407395
|
||||
estimated relative force accuracy = 1.0963718e-06
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 70516 40824
|
||||
Generated 2016 of 2016 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 2 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmmfsw/coul/long, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 16 1.09 1.38032e-07 6
|
||||
Bond: 18 1.09 1.00046e-07 3
|
||||
Bond: 34 1.111 1.11388e-06 10
|
||||
Bond: 39 1.111 4.83041e-08 5
|
||||
Bond: 43 1.111 1.97842e-07 10
|
||||
Bond: 44 1.111 1.71815e-06 10
|
||||
Bond: 59 1.111 8.42509e-08 2
|
||||
Bond: 62 1.111 2.84854e-08 2
|
||||
Bond: 63 1.111 2.14153e-07 46
|
||||
Bond: 64 1.111 1.59305e-07 18
|
||||
Bond: 65 1.08 5.67061e-07 16
|
||||
Bond: 66 1.08 1.43965e-06 4
|
||||
Bond: 67 1 1.81926e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 1.34571e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 2.71955e-07 6530
|
||||
Bond: 75 1 1.46045e-07 10
|
||||
Bond: 79 0.997 5.24499e-07 17
|
||||
Bond: 81 1 1.32984e-07 4
|
||||
Bond: 84 1.04 7.65389e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 5.75241e-07 2
|
||||
Bond: 97 1.325 4.3613e-08 3
|
||||
Angle: 142 104.52 2.67611e-05 3265
|
||||
Per MPI rank memory allocation (min/avg/max) = 76.88 | 77.06 | 77.25 Mbytes
|
||||
Step TotEng E_vdwl E_coul E_long E_dihed PotEng KinEng Temp Press
|
||||
0 -27877.652 3447.5013 144035.68 -182420.51 343.05623 -34213.5 6335.8474 307.44113 -989.27065
|
||||
10 -27879.086 3334.4154 144205.4 -182416.19 348.14696 -34133.566 6254.4808 303.49289 -1211.2863
|
||||
20 -27882.193 3293.7931 144272.04 -182415.87 333.20456 -34116.91 6234.7164 302.53384 -1041.5231
|
||||
30 -27886.779 3177.7183 144344.61 -182409.28 340.77044 -34166.241 6279.462 304.70508 -1538.0247
|
||||
40 -27892.698 3186.4294 144409.85 -182417.01 337.80177 -34097.62 6204.9214 301.08807 -1516.1201
|
||||
50 -27898.215 3198.5531 144426.3 -182405.24 336.58074 -34049.909 6151.6947 298.50529 -1349.4431
|
||||
60 -27900.589 3163.4592 144400.32 -182414.85 341.17705 -34110.926 6210.3369 301.35085 -1695.3697
|
||||
70 -27900.487 3223.7183 144242.71 -182409.21 341.09496 -34188.493 6288.0059 305.11967 -1493.2032
|
||||
80 -27901.07 3274.244 144265.07 -182417.68 344.0409 -34177.343 6276.2725 304.55032 -1273.0263
|
||||
90 -27905.672 3237.6056 144288.71 -182418.22 342.15013 -34187.814 6282.1417 304.83511 -1268.0436
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 16 1.09 3.78281e-07 6
|
||||
Bond: 18 1.09 1.12288e-07 3
|
||||
Bond: 34 1.111 7.60709e-07 10
|
||||
Bond: 39 1.111 2.37855e-07 5
|
||||
Bond: 43 1.111 6.00872e-07 10
|
||||
Bond: 44 1.111 3.75324e-07 10
|
||||
Bond: 59 1.111 1.12311e-07 2
|
||||
Bond: 62 1.111 2.99471e-07 2
|
||||
Bond: 63 1.111 6.10589e-07 46
|
||||
Bond: 64 1.111 4.50733e-07 18
|
||||
Bond: 65 1.08 2.90668e-07 16
|
||||
Bond: 66 1.08 1.61592e-07 4
|
||||
Bond: 67 1 5.4508e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 4.1398e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 1.76706e-06 6530
|
||||
Bond: 75 1 3.96686e-07 10
|
||||
Bond: 79 0.997 7.72922e-07 17
|
||||
Bond: 81 1 1.30673e-07 4
|
||||
Bond: 84 1.04 1.44551e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 1.03526e-07 2
|
||||
Bond: 97 1.325 3.64689e-08 3
|
||||
Angle: 142 104.52 0.000130126 3265
|
||||
100 -27913.241 3159.0676 144299.1 -182414.94 336.48839 -34254.412 6341.1706 307.69943 -1421.2905
|
||||
Loop time of 3.49837 on 4 procs for 100 steps with 10245 atoms
|
||||
|
||||
Performance: 4.939 ns/day, 4.859 hours/ns, 28.585 timesteps/s, 292.851 katom-step/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.4572 | 2.5133 | 2.5634 | 2.6 | 71.84
|
||||
Bond | 0.0040264 | 0.0050718 | 0.0069286 | 1.6 | 0.14
|
||||
Kspace | 0.45979 | 0.50903 | 0.56364 | 5.6 | 14.55
|
||||
Neigh | 0.42029 | 0.42034 | 0.42036 | 0.0 | 12.02
|
||||
Comm | 0.013207 | 0.013292 | 0.013404 | 0.1 | 0.38
|
||||
Output | 0.00026525 | 0.00029549 | 0.00038249 | 0.0 | 0.01
|
||||
Modify | 0.035024 | 0.035546 | 0.03621 | 0.3 | 1.02
|
||||
Other | | 0.001504 | | | 0.04
|
||||
|
||||
Nlocal: 2561.25 ave 2599 max 2520 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 16491.5 ave 16541 max 16442 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 1.99855e+06 ave 2.04035e+06 max 1.95468e+06 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 7994217
|
||||
Ave neighs/atom = 780.30425
|
||||
Ave special neighs/atom = 2.3664226
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
@ -109,4 +109,3 @@ variable skin equal 0.3*${h}
|
||||
neighbor ${skin} bin
|
||||
|
||||
run 6000
|
||||
|
||||
|
||||
@ -5,7 +5,7 @@ LAMMPS data file via write_data, version 24 Dec 2020, timestep = 400000
|
||||
|
||||
9.95143358025075 331.8139610404791 xlo xhi
|
||||
9.95143358025075 331.8139610404791 ylo yhi
|
||||
0 1 zlo zhi
|
||||
-0.5 0.5 zlo zhi
|
||||
0 0 0 xy xz yz
|
||||
|
||||
Atoms # sphere
|
||||
|
||||
75
examples/rheo/balloon/in.rheo.balloon
Normal file
75
examples/rheo/balloon/in.rheo.balloon
Normal file
@ -0,0 +1,75 @@
|
||||
# ------ 2D water balloon ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -40 40 0 80 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
|
||||
region fluid sphere -10 40 0 30 units box side in
|
||||
lattice hex 1.0
|
||||
create_atoms 1 region fluid
|
||||
|
||||
region shell sphere -10 40 0 27 units box side out
|
||||
group shell region shell
|
||||
|
||||
set group shell rheo/status 1
|
||||
set group all vx 0.005 vy -0.04
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
create_bonds many shell shell 1 0 1.5
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# A lower critical strain allows the balloon to pop
|
||||
#bond_coeff 1 1.0 0.05 1.0
|
||||
|
||||
# ------ Drop balloon ------#
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
|
||||
run 30000
|
||||
382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
Normal file
382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
Normal file
@ -0,0 +1,382 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D water balloon ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -40 40 0 80 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
Created orthogonal box = (-40 0 -0.01) to (40 80 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
region fluid sphere -10 40 0 30 units box side in
|
||||
lattice hex 1.0
|
||||
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||
create_atoms 1 region fluid
|
||||
Created 2830 atoms
|
||||
using lattice units in orthogonal box = (-40 0 -0.01) to (40 80 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
region shell sphere -10 40 0 27 units box side out
|
||||
group shell region shell
|
||||
544 atoms in group shell
|
||||
|
||||
set group shell rheo/status 1
|
||||
Setting atom values ...
|
||||
544 settings made for rheo/status
|
||||
set group all vx 0.005 vy -0.04
|
||||
Setting atom values ...
|
||||
2830 settings made for vx
|
||||
2830 settings made for vy
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable kappa equal 0.01*1/${mp}
|
||||
variable kappa equal 0.01*1/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
create_bonds many shell shell 1 0 1.5
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 49 49 1
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair rheo, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) pair rheo/solid, perpetual, trim from (2)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Added 1263 bonds, new total = 1263
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
6 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# A lower critical strain allows the balloon to pop
|
||||
#bond_coeff 1 1.0 0.05 1.0
|
||||
|
||||
# ------ Drop balloon ------#
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 shift surface/detection coordination 22 8
|
||||
fix 1 all rheo 3 quintic 0 shift surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
|
||||
run 30000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 49 49 1
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair rheo, perpetual, half/full from (3)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rheo/solid, perpetual, trim from (1)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.63 | 17.64 | 17.65 Mbytes
|
||||
Step Time KinEng Press Atoms
|
||||
0 0 0.0008125 0.00035927734 2830
|
||||
200 20 0.0008125 0.00035927734 2830
|
||||
400 40 0.0008125 0.00035927734 2830
|
||||
600 60 0.0008125 0.00035927734 2830
|
||||
800 80 0.0008125 0.00035927734 2830
|
||||
1000 100 0.0008125 0.00035927734 2830
|
||||
1200 120 0.0008125 0.00035927734 2830
|
||||
1400 140 0.0008125 0.00035927734 2830
|
||||
1600 160 0.0008125 0.00035927734 2830
|
||||
1800 180 0.0008125 0.00035927734 2830
|
||||
2000 200 0.0008125 0.00035927734 2830
|
||||
2200 220 0.0008125 0.00035927734 2830
|
||||
2400 240 0.00079033569 0.00043037861 2830
|
||||
2600 260 0.0007549229 0.00045188383 2830
|
||||
2800 280 0.00072808836 0.00031695003 2830
|
||||
3000 300 0.0007017958 1.6121754e-05 2830
|
||||
3200 320 0.00067479047 -0.00015725514 2830
|
||||
3400 340 0.00064762254 -0.00023361314 2830
|
||||
3600 360 0.00061960255 -0.00033837679 2830
|
||||
3800 380 0.0005857206 -0.00051770716 2830
|
||||
4000 400 0.00055061733 -0.00070309251 2830
|
||||
4200 420 0.00051884719 -0.0008247795 2830
|
||||
4400 440 0.00049022236 -0.00099918413 2830
|
||||
4600 460 0.00046060011 -0.0010923159 2830
|
||||
4800 480 0.00042900173 -0.0011524571 2830
|
||||
5000 500 0.00039751503 -0.0012586358 2830
|
||||
5200 520 0.00036620054 -0.0013973543 2830
|
||||
5400 540 0.00033130023 -0.0015185231 2830
|
||||
5600 560 0.00030565892 -0.0016159836 2830
|
||||
5800 580 0.00028209836 -0.0016925198 2830
|
||||
6000 600 0.00024695044 -0.0017796892 2830
|
||||
6200 620 0.00021190635 -0.0018706272 2830
|
||||
6400 640 0.0001947093 -0.0019146643 2830
|
||||
6600 660 0.00018903936 -0.0019146199 2830
|
||||
6800 680 0.00017753371 -0.0019390155 2830
|
||||
7000 700 0.00015170593 -0.0020247472 2830
|
||||
7200 720 0.00011509692 -0.0021222209 2830
|
||||
7400 740 7.9861785e-05 -0.0022033181 2830
|
||||
7600 760 6.1350463e-05 -0.0022511971 2830
|
||||
7800 780 6.5269523e-05 -0.0022222806 2830
|
||||
8000 800 8.5709569e-05 -0.0021089664 2830
|
||||
8200 820 0.00011746348 -0.0019351493 2830
|
||||
8400 840 0.00015698134 -0.0017079928 2830
|
||||
8600 860 0.00019758065 -0.0014618965 2830
|
||||
8800 880 0.00023338199 -0.0012365832 2830
|
||||
9000 900 0.00026282353 -0.0010348527 2830
|
||||
9200 920 0.00028604776 -0.00085287884 2830
|
||||
9400 940 0.00030388767 -0.000681122 2830
|
||||
9600 960 0.000317589 -0.00052203521 2830
|
||||
9800 980 0.00032716728 -0.00037501187 2830
|
||||
10000 1000 0.00033270692 -0.00025576132 2830
|
||||
10200 1020 0.00033485986 -0.00016554207 2830
|
||||
10400 1040 0.00033476763 -9.8525417e-05 2830
|
||||
10600 1060 0.00033351922 -5.1166347e-05 2830
|
||||
10800 1080 0.00033161645 -2.0773965e-05 2830
|
||||
11000 1100 0.00032913022 2.2384421e-07 2830
|
||||
11200 1120 0.00032618376 1.2304773e-05 2830
|
||||
11400 1140 0.00032310409 1.3725982e-05 2830
|
||||
11600 1160 0.0003202128 9.0431945e-06 2830
|
||||
11800 1180 0.00031760386 -5.3537879e-07 2830
|
||||
12000 1200 0.00031518884 -1.331708e-05 2830
|
||||
12200 1220 0.00031283958 -3.0838612e-05 2830
|
||||
12400 1240 0.0003104901 -5.0038548e-05 2830
|
||||
12600 1260 0.00030811597 -6.9699925e-05 2830
|
||||
12800 1280 0.00030555782 -8.9972287e-05 2830
|
||||
13000 1300 0.00030256671 -0.00011712941 2830
|
||||
13200 1320 0.00029907961 -0.00015495826 2830
|
||||
13400 1340 0.00029504656 -0.00020292633 2830
|
||||
13600 1360 0.0002905184 -0.00024892421 2830
|
||||
13800 1380 0.00028564542 -0.000295085 2830
|
||||
14000 1400 0.00028073246 -0.00034571956 2830
|
||||
14200 1420 0.00027611457 -0.00039341977 2830
|
||||
14400 1440 0.00027217382 -0.0004281012 2830
|
||||
14600 1460 0.00026919129 -0.00045342545 2830
|
||||
14800 1480 0.00026727674 -0.00047323419 2830
|
||||
15000 1500 0.0002663482 -0.00048423944 2830
|
||||
15200 1520 0.00026616663 -0.0004816085 2830
|
||||
15400 1540 0.00026634862 -0.00047573486 2830
|
||||
15600 1560 0.0002664314 -0.00046803192 2830
|
||||
15800 1580 0.00026603348 -0.00045753668 2830
|
||||
16000 1600 0.00026511015 -0.00044676105 2830
|
||||
16200 1620 0.00026373403 -0.00044075794 2830
|
||||
16400 1640 0.00026217342 -0.00043684036 2830
|
||||
16600 1660 0.0002607038 -0.00042774771 2830
|
||||
16800 1680 0.00025951097 -0.00041603026 2830
|
||||
17000 1700 0.00025869088 -0.00040302996 2830
|
||||
17200 1720 0.00025825588 -0.00038415247 2830
|
||||
17400 1740 0.00025818373 -0.00035742127 2830
|
||||
17600 1760 0.00025843381 -0.00032854722 2830
|
||||
17800 1780 0.00025897836 -0.00029821183 2830
|
||||
18000 1800 0.00025981472 -0.00026108907 2830
|
||||
18200 1820 0.00026095775 -0.00021731058 2830
|
||||
18400 1840 0.00026239688 -0.00017030825 2830
|
||||
18600 1860 0.00026404432 -0.00011868778 2830
|
||||
18800 1880 0.00026574247 -5.9556286e-05 2830
|
||||
19000 1900 0.00026729563 2.3014881e-06 2830
|
||||
19200 1920 0.00026852418 6.2100169e-05 2830
|
||||
19400 1940 0.00026929086 0.00012090325 2830
|
||||
19600 1960 0.0002695407 0.00017904223 2830
|
||||
19800 1980 0.00026929677 0.00023112254 2830
|
||||
20000 2000 0.00026863577 0.0002756697 2830
|
||||
20200 2020 0.00026765699 0.0003158399 2830
|
||||
20400 2040 0.00026646841 0.00035200747 2830
|
||||
20600 2060 0.00026516938 0.00038018442 2830
|
||||
20800 2080 0.00026383495 0.00040179111 2830
|
||||
21000 2100 0.00026252489 0.00042030921 2830
|
||||
21200 2120 0.00026128616 0.00043466976 2830
|
||||
21400 2140 0.00026014896 0.00044221445 2830
|
||||
21600 2160 0.00025912325 0.00044531883 2830
|
||||
21800 2180 0.00025821515 0.00044661709 2830
|
||||
22000 2200 0.00025742576 0.00044409089 2830
|
||||
22200 2220 0.00025674938 0.00043634999 2830
|
||||
22400 2240 0.00025617111 0.00042630344 2830
|
||||
22600 2260 0.0002556791 0.00041561603 2830
|
||||
22800 2280 0.00025525963 0.00040166735 2830
|
||||
23000 2300 0.00025489538 0.00038430419 2830
|
||||
23200 2320 0.00025456861 0.0003669402 2830
|
||||
23400 2340 0.00025426747 0.00034972373 2830
|
||||
23600 2360 0.00025398353 0.0003302242 2830
|
||||
23800 2380 0.00025370842 0.00030993088 2830
|
||||
24000 2400 0.00025344084 0.00029143258 2830
|
||||
24200 2420 0.00025318683 0.00027421708 2830
|
||||
24400 2440 0.0002529591 0.00025603123 2830
|
||||
24600 2460 0.0002527713 0.00023950245 2830
|
||||
24800 2480 0.00025264228 0.00022644812 2830
|
||||
25000 2500 0.00025259021 0.00021540748 2830
|
||||
25200 2520 0.00025262892 0.00020544201 2830
|
||||
25400 2540 0.00025276229 0.00019845807 2830
|
||||
25600 2560 0.0002529876 0.00019449958 2830
|
||||
25800 2580 0.00025329374 0.00019082606 2830
|
||||
26000 2600 0.00025366066 0.00018700064 2830
|
||||
26200 2620 0.00025406164 0.00018426061 2830
|
||||
26400 2640 0.00025446737 0.00018098339 2830
|
||||
26600 2660 0.00025484714 0.00017471869 2830
|
||||
26800 2680 0.00025516604 0.00016565557 2830
|
||||
27000 2700 0.00025538911 0.00015493626 2830
|
||||
27200 2720 0.00025548177 0.00014075592 2830
|
||||
27400 2740 0.00025541168 0.00012205573 2830
|
||||
27600 2760 0.00025514889 0.00010039772 2830
|
||||
27800 2780 0.00025467547 7.7069215e-05 2830
|
||||
28000 2800 0.0002539915 5.1158042e-05 2830
|
||||
28200 2820 0.00025312083 2.3468384e-05 2830
|
||||
28400 2840 0.00025211323 -3.2184465e-06 2830
|
||||
28600 2860 0.00025104366 -2.7726301e-05 2830
|
||||
28800 2880 0.00025000263 -5.0202987e-05 2830
|
||||
29000 2900 0.00024907814 -6.9244776e-05 2830
|
||||
29200 2920 0.00024833815 -8.2874516e-05 2830
|
||||
29400 2940 0.0002478155 -9.1854992e-05 2830
|
||||
29600 2960 0.00024750313 -9.766055e-05 2830
|
||||
29800 2980 0.00024735538 -9.9681291e-05 2830
|
||||
30000 3000 0.00024730191 -9.818759e-05 2830
|
||||
Loop time of 177.982 on 4 procs for 30000 steps with 2830 atoms
|
||||
|
||||
Performance: 1456330.235 tau/day, 168.557 timesteps/s, 477.016 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 22.913 | 27.061 | 34.594 | 87.2 | 15.20
|
||||
Bond | 0.22386 | 0.26159 | 0.30792 | 6.0 | 0.15
|
||||
Neigh | 0.84412 | 0.84509 | 0.8462 | 0.1 | 0.47
|
||||
Comm | 0.50015 | 0.55579 | 0.60346 | 5.2 | 0.31
|
||||
Output | 0.65854 | 0.69412 | 0.72473 | 2.8 | 0.39
|
||||
Modify | 133.13 | 136 | 137.38 | 14.5 | 76.41
|
||||
Other | | 12.57 | | | 7.06
|
||||
|
||||
Nlocal: 707.5 ave 1576 max 53 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 164.75 ave 239 max 94 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 12307.8 ave 27380 max 983 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
FullNghs: 23517 ave 53040 max 1502 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 94068
|
||||
Ave neighs/atom = 33.239576
|
||||
Ave special neighs/atom = 0.89257951
|
||||
Neighbor list builds = 783
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:58
|
||||
76
examples/rheo/dam-break/in.rheo.dam.break
Normal file
76
examples/rheo/dam-break/in.rheo.dam.break
Normal file
@ -0,0 +1,76 @@
|
||||
# ------ 2D dam break ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style rheo
|
||||
boundary f s p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
# ------ Create simulation box ------ #
|
||||
|
||||
variable n equal 1.0
|
||||
variable cut equal 2.2
|
||||
variable dx equal 3.0
|
||||
|
||||
region box block -1 150 -1 80 -0.1 0.1 units box
|
||||
create_box 2 box
|
||||
lattice hex ${n}
|
||||
|
||||
region fluid block $(xlo+v_dx+1.0) $(xlo+40.0) $(ylo+v_dx+1.0) $(yhi-20.0) EDGE EDGE units box
|
||||
region walls1 block $(xlo+v_dx) $(xhi-v_dx) $(ylo+v_dx) $(yhi-v_dx) EDGE EDGE side out units box
|
||||
region walls2 block EDGE EDGE EDGE $(yhi-v_dx) EDGE EDGE side in units box
|
||||
region walls intersect 2 walls1 walls2
|
||||
|
||||
create_atoms 1 region fluid
|
||||
create_atoms 2 region walls
|
||||
|
||||
group fluid type 1
|
||||
group rig type 2
|
||||
|
||||
# ------ Model parameters ------ #
|
||||
|
||||
variable rho0 equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable cs equal 1.0
|
||||
variable zeta equal 0.1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.1
|
||||
variable Dr equal 0.1
|
||||
|
||||
mass 1 ${mp}
|
||||
mass 2 $(2*v_mp)
|
||||
set group all rheo/rho ${rho0}
|
||||
|
||||
set group all rheo/status 0
|
||||
set group rig rheo/status 1
|
||||
|
||||
timestep ${dt_max}
|
||||
|
||||
pair_style rheo ${cut} artificial/visc ${zeta} #rho/damp ${Dr}
|
||||
pair_coeff * *
|
||||
|
||||
# ------ Fixes & computes ------ #
|
||||
|
||||
fix 1 all rheo ${cut} quintic 10 &
|
||||
surface/detection coordination 22 8 &
|
||||
rho/sum
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all gravity 1e-3 vector 0 -1 0
|
||||
fix 5 rig setforce 0.0 0.0 0.0
|
||||
fix 6 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute p all rheo/property/atom pressure
|
||||
compute surf all rheo/property/atom surface
|
||||
compute sn all rheo/property/atom surface/n/x surface/n/y
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 20
|
||||
thermo_style custom step time ke press
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho c_surf c_p c_sn[*]
|
||||
|
||||
run 30000
|
||||
1694
examples/rheo/dam-break/log.17Apr2024.dam.g++.4
Normal file
1694
examples/rheo/dam-break/log.17Apr2024.dam.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
82
examples/rheo/ice-cubes/in.rheo.ice.cubes
Normal file
82
examples/rheo/ice-cubes/in.rheo.ice.cubes
Normal file
@ -0,0 +1,82 @@
|
||||
# ------ 2D Ice Cube Pour ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
region box block -25 25 0 100 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
|
||||
region fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
lattice sq 1.0
|
||||
create_atoms 1 region fluid
|
||||
|
||||
set group all sph/e 8.0
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# ------ Pour particles ------#
|
||||
|
||||
molecule my_mol "square.mol"
|
||||
|
||||
# Wall region extends far enough in z to avoid contact
|
||||
region wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
|
||||
region drop block -16 16 70 90 EDGE EDGE side in units box
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
thermal &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} &
|
||||
specific/heat * constant ${Cv} &
|
||||
Tfreeze * constant ${Tf} &
|
||||
latent/heat * constant ${L} &
|
||||
react 1.5 1
|
||||
fix 5 all wall/region wall harmonic 1.0 1.0 1.0
|
||||
fix 6 all gravity 5e-4 vector 0 -1 0
|
||||
fix 7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
|
||||
fix 8 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
|
||||
|
||||
run 30000
|
||||
379
examples/rheo/ice-cubes/log.17Apr2024.ice.g++.4
Normal file
379
examples/rheo/ice-cubes/log.17Apr2024.ice.g++.4
Normal file
@ -0,0 +1,379 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
|
||||
# ------ 2D Ice Cube Pour ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
region box block -25 25 0 100 -0.01 0.01 units box
|
||||
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
|
||||
Created orthogonal box = (-25 0 -0.01) to (25 100 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
region fluid block $(xlo+1) $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 $(xhi-1) $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 24 $(ylo+1) $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 24 1 $(ylo+30) EDGE EDGE units box
|
||||
region fluid block -24 24 1 30 EDGE EDGE units box
|
||||
lattice sq 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
create_atoms 1 region fluid
|
||||
Created 1470 atoms
|
||||
using lattice units in orthogonal box = (-25 0 -0.01) to (25 100 0.01)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
set group all sph/e 8.0
|
||||
Setting atom values ...
|
||||
1470 settings made for sph/e
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.01*${rho0}/${mp}
|
||||
variable kappa equal 0.01*1/${mp}
|
||||
variable kappa equal 0.01*1/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 1.0
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
bond_style bpm/spring
|
||||
bond_coeff 1 1.0 1.0 1.0
|
||||
|
||||
# ------ Pour particles ------#
|
||||
|
||||
molecule my_mol "square.mol"
|
||||
Read molecule template my_mol:
|
||||
#Made with create_mol.py
|
||||
1 molecules
|
||||
0 fragments
|
||||
100 atoms with max type 1
|
||||
342 bonds with max type 1
|
||||
0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
|
||||
# Wall region extends far enough in z to avoid contact
|
||||
region wall block EDGE EDGE EDGE EDGE -5 5 side in open 4 units box
|
||||
region drop block -16 16 70 90 EDGE EDGE side in units box
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.01 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 1 react 1.5 1
|
||||
fix 5 all wall/region wall harmonic 1.0 1.0 1.0
|
||||
fix 6 all gravity 5e-4 vector 0 -1 0
|
||||
fix 7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
|
||||
WARNING: Molecule attributes do not match system attributes (../molecule.cpp:1881)
|
||||
fix 8 all enforce2d
|
||||
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond all nbond/atom
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond c_rho
|
||||
|
||||
run 30000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
- @article{ApplMathModel.130.310,
|
||||
title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
|
||||
journal = {Applied Mathematical Modelling},
|
||||
volume = {130},
|
||||
pages = {310-326},
|
||||
year = {2024},
|
||||
issn = {0307-904X},
|
||||
doi = {https://doi.org/10.1016/j.apm.2024.02.027},
|
||||
author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 31 61 1
|
||||
7 neighbor lists, perpetual/occasional/extra = 6 1 0
|
||||
(1) pair rheo, perpetual, half/full from (3)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rheo/solid, perpetual, trim from (4)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(7) fix rheo/thermal, occasional, trim from (4)
|
||||
attributes: half, newton off, cut 3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.53 | 15.61 | 15.69 Mbytes
|
||||
Step Time KinEng Press Atoms
|
||||
0 0 0 0 1470
|
||||
200 20 5.6002982e-05 3.4434234e-05 1570
|
||||
400 40 8.2173099e-05 8.6171768e-05 1570
|
||||
600 60 8.019018e-05 0.00010750355 1570
|
||||
800 80 0.00013866953 0.00010265608 1570
|
||||
1000 100 0.00018965028 8.1985605e-05 1570
|
||||
1200 120 0.00022033242 7.4736443e-05 1670
|
||||
1400 140 0.00030767062 0.00011264333 1670
|
||||
1600 160 0.00040770127 0.00018779992 1670
|
||||
1800 180 0.00047476332 0.00023153009 1670
|
||||
2000 200 0.00059116774 0.00027200445 1670
|
||||
2200 220 0.0007151733 0.0002919963 1770
|
||||
2400 240 0.00083392135 0.00029757889 1770
|
||||
2600 260 0.00099653466 0.00036547269 1770
|
||||
2800 280 0.0011964069 0.00045983458 1770
|
||||
3000 300 0.0013716953 0.00055013647 1770
|
||||
3200 320 0.0015174096 0.00064203572 1870
|
||||
3400 340 0.0016539743 0.00086671622 1870
|
||||
3600 360 0.0015887858 0.00066353749 1870
|
||||
3800 380 0.0016451684 0.00070551483 1870
|
||||
4000 400 0.0017330971 0.00080722283 1870
|
||||
4200 420 0.001812193 0.00073573903 1970
|
||||
4400 440 0.001755871 0.0010621909 1970
|
||||
4600 460 0.0016190772 0.00072913706 1970
|
||||
4800 480 0.0015741931 0.00073524088 1970
|
||||
5000 500 0.0016488815 0.00088684275 1970
|
||||
5200 520 0.0017213288 0.00077042378 2070
|
||||
5400 540 0.0018509598 0.0010219434 2070
|
||||
5600 560 0.0020251064 0.00083182483 2070
|
||||
5800 580 0.0022473255 0.00095076144 2070
|
||||
6000 600 0.0024843519 0.0011247014 2070
|
||||
6200 620 0.0022282321 0.0018105932 2170
|
||||
6400 640 0.0020289063 0.0014158497 2170
|
||||
6600 660 0.002145241 0.0011359383 2170
|
||||
6800 680 0.0024313937 0.0016475504 2170
|
||||
7000 700 0.0021000599 0.0020983745 2170
|
||||
7200 720 0.0019137235 0.0010439152 2270
|
||||
7400 740 0.0018801367 0.00095436448 2270
|
||||
7600 760 0.0017979449 0.0011184039 2270
|
||||
7800 780 0.0018005205 0.0009243205 2270
|
||||
8000 800 0.0017827073 0.0013671228 2270
|
||||
8200 820 0.0018387108 0.0015426012 2270
|
||||
8400 840 0.0016000788 0.0016751514 2270
|
||||
8600 860 0.0013954964 0.0016884335 2270
|
||||
8800 880 0.0013283728 0.0012399398 2270
|
||||
9000 900 0.001389385 0.0012968496 2270
|
||||
9200 920 0.0012295438 0.0012995821 2270
|
||||
9400 940 0.0010522655 0.00082245528 2270
|
||||
9600 960 0.00097085496 0.00053833131 2270
|
||||
9800 980 0.0009398987 0.00063467387 2270
|
||||
10000 1000 0.00092710392 0.00059494446 2270
|
||||
10200 1020 0.00095545471 0.00074560644 2270
|
||||
10400 1040 0.0009645841 0.00085429807 2270
|
||||
10600 1060 0.00064037148 0.0017222246 2270
|
||||
10800 1080 0.00046790978 0.00088204234 2270
|
||||
11000 1100 0.00030106229 0.00074950209 2270
|
||||
11200 1120 0.00027746016 0.00052831745 2270
|
||||
11400 1140 0.0002533348 0.0006272715 2270
|
||||
11600 1160 0.00021825085 0.00029691552 2270
|
||||
11800 1180 0.0001451308 0.00015037478 2270
|
||||
12000 1200 0.0001314823 0.00017227174 2270
|
||||
12200 1220 0.00013693632 0.00017791384 2270
|
||||
12400 1240 0.00014987347 0.0002286677 2270
|
||||
12600 1260 0.00015092598 0.0003698436 2270
|
||||
12800 1280 0.0001291653 0.00047229532 2270
|
||||
13000 1300 0.00011949988 0.00049560375 2270
|
||||
13200 1320 0.00011694665 0.00057542084 2270
|
||||
13400 1340 9.6164519e-05 0.00062714755 2270
|
||||
13600 1360 8.4517591e-05 0.00044156913 2270
|
||||
13800 1380 0.00019140516 0.0003264745 2270
|
||||
14000 1400 0.00013868599 0.00037753497 2270
|
||||
14200 1420 9.3701636e-05 0.00031517848 2270
|
||||
14400 1440 6.7389077e-05 0.0002946861 2270
|
||||
14600 1460 5.3640086e-05 0.00026650711 2270
|
||||
14800 1480 4.2699992e-05 0.00023789279 2270
|
||||
15000 1500 5.3012016e-05 0.00019933234 2270
|
||||
15200 1520 5.8834197e-05 0.00022407007 2270
|
||||
15400 1540 5.0899982e-05 0.00029695531 2270
|
||||
15600 1560 3.0476742e-05 0.00039119066 2270
|
||||
15800 1580 1.6633264e-05 0.00033770401 2270
|
||||
16000 1600 1.098906e-05 0.00036684894 2270
|
||||
16200 1620 1.464848e-05 0.00036449759 2270
|
||||
16400 1640 1.9598429e-05 0.00021056689 2270
|
||||
16600 1660 1.2644955e-05 0.00020781781 2270
|
||||
16800 1680 8.8428553e-06 0.000165 2270
|
||||
17000 1700 8.8971439e-06 0.00012266475 2270
|
||||
17200 1720 1.7032781e-05 0.00019873443 2270
|
||||
17400 1740 1.9448563e-05 0.00025661663 2270
|
||||
17600 1760 1.3714713e-05 0.000324022 2270
|
||||
17800 1780 9.1326468e-06 0.00031392513 2270
|
||||
18000 1800 9.2464802e-06 0.00029729527 2270
|
||||
18200 1820 1.5553042e-05 0.00027488475 2270
|
||||
18400 1840 1.4132933e-05 0.00019565459 2270
|
||||
18600 1860 9.4734832e-06 0.00016716988 2270
|
||||
18800 1880 5.5115145e-06 0.00013728033 2270
|
||||
19000 1900 8.268812e-06 0.00015119605 2270
|
||||
19200 1920 1.2470136e-05 0.00020222131 2270
|
||||
19400 1940 9.9387775e-06 0.00024503373 2270
|
||||
19600 1960 5.4241999e-06 0.00026921858 2270
|
||||
19800 1980 2.7987348e-06 0.00026201267 2270
|
||||
20000 2000 6.272538e-06 0.00025626323 2270
|
||||
20200 2020 8.0157781e-06 0.000220139 2270
|
||||
20400 2040 6.1652093e-06 0.00017089058 2270
|
||||
20600 2060 2.9967592e-06 0.00014582864 2270
|
||||
20800 2080 3.016678e-06 0.000148629 2270
|
||||
21000 2100 7.287645e-06 0.00016486102 2270
|
||||
21200 2120 8.6905277e-06 0.00020276916 2270
|
||||
21400 2140 6.8453018e-06 0.00023156153 2270
|
||||
21600 2160 3.3853799e-06 0.0002432462 2270
|
||||
21800 2180 4.1241209e-06 0.00022829024 2270
|
||||
22000 2200 7.0802396e-06 0.00020784823 2270
|
||||
22200 2220 7.3361691e-06 0.00018114134 2270
|
||||
22400 2240 5.0764593e-06 0.00014351106 2270
|
||||
22600 2260 2.7487537e-06 0.00012919872 2270
|
||||
22800 2280 4.620167e-06 0.00013746218 2270
|
||||
23000 2300 6.9819357e-06 0.00015985102 2270
|
||||
23200 2320 6.8923916e-06 0.00018713045 2270
|
||||
23400 2340 4.1795088e-06 0.00019846682 2270
|
||||
23600 2360 2.2871028e-06 0.00021068421 2270
|
||||
23800 2380 3.862046e-06 0.00019553306 2270
|
||||
24000 2400 5.2448555e-06 0.00017398041 2270
|
||||
24200 2420 4.7565441e-06 0.00015008142 2270
|
||||
24400 2440 2.2952135e-06 0.00012747106 2270
|
||||
24600 2460 2.1575617e-06 0.00012516996 2270
|
||||
24800 2480 4.1777868e-06 0.0001331902 2270
|
||||
25000 2500 5.5679133e-06 0.00015504562 2270
|
||||
25200 2520 4.5758741e-06 0.00017146032 2270
|
||||
25400 2540 2.3403277e-06 0.00017611666 2270
|
||||
25600 2560 2.7029302e-06 0.00016850788 2270
|
||||
25800 2580 4.3601102e-06 0.00015884642 2270
|
||||
26000 2600 5.2244249e-06 0.00013793898 2270
|
||||
26200 2620 3.4577672e-06 0.00012395875 2270
|
||||
26400 2640 2.361577e-06 0.00011600057 2270
|
||||
26600 2660 2.8515644e-06 0.00011277063 2270
|
||||
26800 2680 4.0851213e-06 0.0001290832 2270
|
||||
27000 2700 4.2579644e-06 0.0001476495 2270
|
||||
27200 2720 2.6593858e-06 0.00015977745 2270
|
||||
27400 2740 1.990115e-06 0.00015612787 2270
|
||||
27600 2760 2.6756835e-06 0.00014913772 2270
|
||||
27800 2780 3.9032806e-06 0.00014014763 2270
|
||||
28000 2800 3.2729446e-06 0.00012216846 2270
|
||||
28200 2820 1.9357278e-06 0.00011078621 2270
|
||||
28400 2840 1.7094832e-06 0.00010910509 2270
|
||||
28600 2860 2.8731406e-06 0.00011179644 2270
|
||||
28800 2880 3.7062354e-06 0.00012254091 2270
|
||||
29000 2900 2.7844262e-06 0.00013060331 2270
|
||||
29200 2920 1.7680655e-06 0.00013797514 2270
|
||||
29400 2940 1.706873e-06 0.0001350685 2270
|
||||
29600 2960 2.8764562e-06 0.00012428508 2270
|
||||
29800 2980 3.1502029e-06 0.00011456718 2270
|
||||
30000 3000 2.1833409e-06 0.00010317469 2270
|
||||
Loop time of 165.611 on 4 procs for 30000 steps with 2270 atoms
|
||||
|
||||
Performance: 1565111.240 tau/day, 181.147 timesteps/s, 411.204 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.63183 | 21.226 | 42.266 | 444.6 | 12.82
|
||||
Bond | 0.095073 | 0.17799 | 0.27877 | 17.0 | 0.11
|
||||
Neigh | 2.0745 | 2.0781 | 2.0822 | 0.2 | 1.25
|
||||
Comm | 0.32024 | 0.38703 | 0.45564 | 8.1 | 0.23
|
||||
Output | 0.60459 | 0.76798 | 0.93724 | 18.6 | 0.46
|
||||
Modify | 119.85 | 140.76 | 161.36 | 172.2 | 85.00
|
||||
Other | | 0.2124 | | | 0.13
|
||||
|
||||
Nlocal: 567.5 ave 1139 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 75.5 ave 152 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 9238.25 ave 18490 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 17945 ave 35917 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 71780
|
||||
Ave neighs/atom = 31.621145
|
||||
Ave special neighs/atom = 0.22026432
|
||||
Neighbor list builds = 2071
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:02:45
|
||||
658
examples/rheo/ice-cubes/square.mol
Normal file
658
examples/rheo/ice-cubes/square.mol
Normal file
@ -0,0 +1,658 @@
|
||||
#Made with create_mol.py
|
||||
|
||||
100 atoms
|
||||
342 bonds
|
||||
|
||||
Coords
|
||||
#ID x y z
|
||||
1 -4 -4 0
|
||||
2 -3 -4 0
|
||||
3 -2 -4 0
|
||||
4 -1 -4 0
|
||||
5 0 -4 0
|
||||
6 1 -4 0
|
||||
7 2 -4 0
|
||||
8 3 -4 0
|
||||
9 4 -4 0
|
||||
10 5 -4 0
|
||||
11 -4 -3 0
|
||||
12 -3 -3 0
|
||||
13 -2 -3 0
|
||||
14 -1 -3 0
|
||||
15 0 -3 0
|
||||
16 1 -3 0
|
||||
17 2 -3 0
|
||||
18 3 -3 0
|
||||
19 4 -3 0
|
||||
20 5 -3 0
|
||||
21 -4 -2 0
|
||||
22 -3 -2 0
|
||||
23 -2 -2 0
|
||||
24 -1 -2 0
|
||||
25 0 -2 0
|
||||
26 1 -2 0
|
||||
27 2 -2 0
|
||||
28 3 -2 0
|
||||
29 4 -2 0
|
||||
30 5 -2 0
|
||||
31 -4 -1 0
|
||||
32 -3 -1 0
|
||||
33 -2 -1 0
|
||||
34 -1 -1 0
|
||||
35 0 -1 0
|
||||
36 1 -1 0
|
||||
37 2 -1 0
|
||||
38 3 -1 0
|
||||
39 4 -1 0
|
||||
40 5 -1 0
|
||||
41 -4 0 0
|
||||
42 -3 0 0
|
||||
43 -2 0 0
|
||||
44 -1 0 0
|
||||
45 0 0 0
|
||||
46 1 0 0
|
||||
47 2 0 0
|
||||
48 3 0 0
|
||||
49 4 0 0
|
||||
50 5 0 0
|
||||
51 -4 1 0
|
||||
52 -3 1 0
|
||||
53 -2 1 0
|
||||
54 -1 1 0
|
||||
55 0 1 0
|
||||
56 1 1 0
|
||||
57 2 1 0
|
||||
58 3 1 0
|
||||
59 4 1 0
|
||||
60 5 1 0
|
||||
61 -4 2 0
|
||||
62 -3 2 0
|
||||
63 -2 2 0
|
||||
64 -1 2 0
|
||||
65 0 2 0
|
||||
66 1 2 0
|
||||
67 2 2 0
|
||||
68 3 2 0
|
||||
69 4 2 0
|
||||
70 5 2 0
|
||||
71 -4 3 0
|
||||
72 -3 3 0
|
||||
73 -2 3 0
|
||||
74 -1 3 0
|
||||
75 0 3 0
|
||||
76 1 3 0
|
||||
77 2 3 0
|
||||
78 3 3 0
|
||||
79 4 3 0
|
||||
80 5 3 0
|
||||
81 -4 4 0
|
||||
82 -3 4 0
|
||||
83 -2 4 0
|
||||
84 -1 4 0
|
||||
85 0 4 0
|
||||
86 1 4 0
|
||||
87 2 4 0
|
||||
88 3 4 0
|
||||
89 4 4 0
|
||||
90 5 4 0
|
||||
91 -4 5 0
|
||||
92 -3 5 0
|
||||
93 -2 5 0
|
||||
94 -1 5 0
|
||||
95 0 5 0
|
||||
96 1 5 0
|
||||
97 2 5 0
|
||||
98 3 5 0
|
||||
99 4 5 0
|
||||
100 5 5 0
|
||||
|
||||
Types
|
||||
#ID type
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
64 1
|
||||
65 1
|
||||
66 1
|
||||
67 1
|
||||
68 1
|
||||
69 1
|
||||
70 1
|
||||
71 1
|
||||
72 1
|
||||
73 1
|
||||
74 1
|
||||
75 1
|
||||
76 1
|
||||
77 1
|
||||
78 1
|
||||
79 1
|
||||
80 1
|
||||
81 1
|
||||
82 1
|
||||
83 1
|
||||
84 1
|
||||
85 1
|
||||
86 1
|
||||
87 1
|
||||
88 1
|
||||
89 1
|
||||
90 1
|
||||
91 1
|
||||
92 1
|
||||
93 1
|
||||
94 1
|
||||
95 1
|
||||
96 1
|
||||
97 1
|
||||
98 1
|
||||
99 1
|
||||
100 1
|
||||
|
||||
Masses
|
||||
#ID mass
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
47 1
|
||||
48 1
|
||||
49 1
|
||||
50 1
|
||||
51 1
|
||||
52 1
|
||||
53 1
|
||||
54 1
|
||||
55 1
|
||||
56 1
|
||||
57 1
|
||||
58 1
|
||||
59 1
|
||||
60 1
|
||||
61 1
|
||||
62 1
|
||||
63 1
|
||||
64 1
|
||||
65 1
|
||||
66 1
|
||||
67 1
|
||||
68 1
|
||||
69 1
|
||||
70 1
|
||||
71 1
|
||||
72 1
|
||||
73 1
|
||||
74 1
|
||||
75 1
|
||||
76 1
|
||||
77 1
|
||||
78 1
|
||||
79 1
|
||||
80 1
|
||||
81 1
|
||||
82 1
|
||||
83 1
|
||||
84 1
|
||||
85 1
|
||||
86 1
|
||||
87 1
|
||||
88 1
|
||||
89 1
|
||||
90 1
|
||||
91 1
|
||||
92 1
|
||||
93 1
|
||||
94 1
|
||||
95 1
|
||||
96 1
|
||||
97 1
|
||||
98 1
|
||||
99 1
|
||||
100 1
|
||||
|
||||
Bonds
|
||||
#ID type atom1 atom2
|
||||
1 1 1 2
|
||||
2 1 1 11
|
||||
3 1 1 12
|
||||
4 1 2 3
|
||||
5 1 2 11
|
||||
6 1 2 12
|
||||
7 1 2 13
|
||||
8 1 3 4
|
||||
9 1 3 12
|
||||
10 1 3 13
|
||||
11 1 3 14
|
||||
12 1 4 5
|
||||
13 1 4 13
|
||||
14 1 4 14
|
||||
15 1 4 15
|
||||
16 1 5 6
|
||||
17 1 5 14
|
||||
18 1 5 15
|
||||
19 1 5 16
|
||||
20 1 6 7
|
||||
21 1 6 15
|
||||
22 1 6 16
|
||||
23 1 6 17
|
||||
24 1 7 8
|
||||
25 1 7 16
|
||||
26 1 7 17
|
||||
27 1 7 18
|
||||
28 1 8 9
|
||||
29 1 8 17
|
||||
30 1 8 18
|
||||
31 1 8 19
|
||||
32 1 9 10
|
||||
33 1 9 18
|
||||
34 1 9 19
|
||||
35 1 9 20
|
||||
36 1 10 19
|
||||
37 1 10 20
|
||||
38 1 11 21
|
||||
39 1 11 12
|
||||
40 1 11 22
|
||||
41 1 12 21
|
||||
42 1 12 13
|
||||
43 1 12 22
|
||||
44 1 12 23
|
||||
45 1 13 22
|
||||
46 1 13 23
|
||||
47 1 13 14
|
||||
48 1 13 24
|
||||
49 1 14 23
|
||||
50 1 14 24
|
||||
51 1 14 15
|
||||
52 1 14 25
|
||||
53 1 15 24
|
||||
54 1 15 16
|
||||
55 1 15 25
|
||||
56 1 15 26
|
||||
57 1 16 25
|
||||
58 1 16 26
|
||||
59 1 16 17
|
||||
60 1 16 27
|
||||
61 1 17 26
|
||||
62 1 17 18
|
||||
63 1 17 27
|
||||
64 1 17 28
|
||||
65 1 18 27
|
||||
66 1 18 28
|
||||
67 1 18 19
|
||||
68 1 18 29
|
||||
69 1 19 28
|
||||
70 1 19 29
|
||||
71 1 19 20
|
||||
72 1 19 30
|
||||
73 1 20 29
|
||||
74 1 20 30
|
||||
75 1 21 22
|
||||
76 1 21 31
|
||||
77 1 21 32
|
||||
78 1 22 23
|
||||
79 1 22 31
|
||||
80 1 22 32
|
||||
81 1 22 33
|
||||
82 1 23 24
|
||||
83 1 23 32
|
||||
84 1 23 33
|
||||
85 1 23 34
|
||||
86 1 24 25
|
||||
87 1 24 33
|
||||
88 1 24 34
|
||||
89 1 24 35
|
||||
90 1 25 26
|
||||
91 1 25 34
|
||||
92 1 25 35
|
||||
93 1 25 36
|
||||
94 1 26 27
|
||||
95 1 26 35
|
||||
96 1 26 36
|
||||
97 1 26 37
|
||||
98 1 27 28
|
||||
99 1 27 36
|
||||
100 1 27 37
|
||||
101 1 27 38
|
||||
102 1 28 29
|
||||
103 1 28 37
|
||||
104 1 28 38
|
||||
105 1 28 39
|
||||
106 1 29 30
|
||||
107 1 29 38
|
||||
108 1 29 39
|
||||
109 1 29 40
|
||||
110 1 30 39
|
||||
111 1 30 40
|
||||
112 1 31 32
|
||||
113 1 31 41
|
||||
114 1 31 42
|
||||
115 1 32 33
|
||||
116 1 32 41
|
||||
117 1 32 42
|
||||
118 1 32 43
|
||||
119 1 33 34
|
||||
120 1 33 42
|
||||
121 1 33 43
|
||||
122 1 33 44
|
||||
123 1 34 35
|
||||
124 1 34 43
|
||||
125 1 34 44
|
||||
126 1 34 45
|
||||
127 1 35 36
|
||||
128 1 35 44
|
||||
129 1 35 45
|
||||
130 1 35 46
|
||||
131 1 36 37
|
||||
132 1 36 45
|
||||
133 1 36 46
|
||||
134 1 36 47
|
||||
135 1 37 38
|
||||
136 1 37 46
|
||||
137 1 37 47
|
||||
138 1 37 48
|
||||
139 1 38 39
|
||||
140 1 38 47
|
||||
141 1 38 48
|
||||
142 1 38 49
|
||||
143 1 39 40
|
||||
144 1 39 48
|
||||
145 1 39 49
|
||||
146 1 39 50
|
||||
147 1 40 49
|
||||
148 1 40 50
|
||||
149 1 41 51
|
||||
150 1 41 42
|
||||
151 1 41 52
|
||||
152 1 42 51
|
||||
153 1 42 43
|
||||
154 1 42 52
|
||||
155 1 42 53
|
||||
156 1 43 52
|
||||
157 1 43 53
|
||||
158 1 43 44
|
||||
159 1 43 54
|
||||
160 1 44 53
|
||||
161 1 44 54
|
||||
162 1 44 45
|
||||
163 1 44 55
|
||||
164 1 45 54
|
||||
165 1 45 46
|
||||
166 1 45 55
|
||||
167 1 45 56
|
||||
168 1 46 55
|
||||
169 1 46 56
|
||||
170 1 46 47
|
||||
171 1 46 57
|
||||
172 1 47 56
|
||||
173 1 47 48
|
||||
174 1 47 57
|
||||
175 1 47 58
|
||||
176 1 48 57
|
||||
177 1 48 58
|
||||
178 1 48 49
|
||||
179 1 48 59
|
||||
180 1 49 58
|
||||
181 1 49 59
|
||||
182 1 49 50
|
||||
183 1 49 60
|
||||
184 1 50 59
|
||||
185 1 50 60
|
||||
186 1 51 52
|
||||
187 1 51 61
|
||||
188 1 51 62
|
||||
189 1 52 53
|
||||
190 1 52 61
|
||||
191 1 52 62
|
||||
192 1 52 63
|
||||
193 1 53 54
|
||||
194 1 53 62
|
||||
195 1 53 63
|
||||
196 1 53 64
|
||||
197 1 54 55
|
||||
198 1 54 63
|
||||
199 1 54 64
|
||||
200 1 54 65
|
||||
201 1 55 56
|
||||
202 1 55 64
|
||||
203 1 55 65
|
||||
204 1 55 66
|
||||
205 1 56 57
|
||||
206 1 56 65
|
||||
207 1 56 66
|
||||
208 1 56 67
|
||||
209 1 57 58
|
||||
210 1 57 66
|
||||
211 1 57 67
|
||||
212 1 57 68
|
||||
213 1 58 59
|
||||
214 1 58 67
|
||||
215 1 58 68
|
||||
216 1 58 69
|
||||
217 1 59 60
|
||||
218 1 59 68
|
||||
219 1 59 69
|
||||
220 1 59 70
|
||||
221 1 60 69
|
||||
222 1 60 70
|
||||
223 1 61 71
|
||||
224 1 61 62
|
||||
225 1 61 72
|
||||
226 1 62 71
|
||||
227 1 62 63
|
||||
228 1 62 72
|
||||
229 1 62 73
|
||||
230 1 63 72
|
||||
231 1 63 73
|
||||
232 1 63 64
|
||||
233 1 63 74
|
||||
234 1 64 73
|
||||
235 1 64 74
|
||||
236 1 64 65
|
||||
237 1 64 75
|
||||
238 1 65 74
|
||||
239 1 65 66
|
||||
240 1 65 75
|
||||
241 1 65 76
|
||||
242 1 66 75
|
||||
243 1 66 76
|
||||
244 1 66 67
|
||||
245 1 66 77
|
||||
246 1 67 76
|
||||
247 1 67 68
|
||||
248 1 67 77
|
||||
249 1 67 78
|
||||
250 1 68 77
|
||||
251 1 68 78
|
||||
252 1 68 69
|
||||
253 1 68 79
|
||||
254 1 69 78
|
||||
255 1 69 79
|
||||
256 1 69 70
|
||||
257 1 69 80
|
||||
258 1 70 79
|
||||
259 1 70 80
|
||||
260 1 71 72
|
||||
261 1 71 81
|
||||
262 1 71 82
|
||||
263 1 72 73
|
||||
264 1 72 81
|
||||
265 1 72 82
|
||||
266 1 72 83
|
||||
267 1 73 74
|
||||
268 1 73 82
|
||||
269 1 73 83
|
||||
270 1 73 84
|
||||
271 1 74 75
|
||||
272 1 74 83
|
||||
273 1 74 84
|
||||
274 1 74 85
|
||||
275 1 75 76
|
||||
276 1 75 84
|
||||
277 1 75 85
|
||||
278 1 75 86
|
||||
279 1 76 77
|
||||
280 1 76 85
|
||||
281 1 76 86
|
||||
282 1 76 87
|
||||
283 1 77 78
|
||||
284 1 77 86
|
||||
285 1 77 87
|
||||
286 1 77 88
|
||||
287 1 78 79
|
||||
288 1 78 87
|
||||
289 1 78 88
|
||||
290 1 78 89
|
||||
291 1 79 80
|
||||
292 1 79 88
|
||||
293 1 79 89
|
||||
294 1 79 90
|
||||
295 1 80 89
|
||||
296 1 80 90
|
||||
297 1 81 82
|
||||
298 1 81 91
|
||||
299 1 81 92
|
||||
300 1 82 83
|
||||
301 1 82 91
|
||||
302 1 82 92
|
||||
303 1 82 93
|
||||
304 1 83 84
|
||||
305 1 83 92
|
||||
306 1 83 93
|
||||
307 1 83 94
|
||||
308 1 84 85
|
||||
309 1 84 93
|
||||
310 1 84 94
|
||||
311 1 84 95
|
||||
312 1 85 86
|
||||
313 1 85 94
|
||||
314 1 85 95
|
||||
315 1 85 96
|
||||
316 1 86 87
|
||||
317 1 86 95
|
||||
318 1 86 96
|
||||
319 1 86 97
|
||||
320 1 87 88
|
||||
321 1 87 96
|
||||
322 1 87 97
|
||||
323 1 87 98
|
||||
324 1 88 89
|
||||
325 1 88 97
|
||||
326 1 88 98
|
||||
327 1 88 99
|
||||
328 1 89 90
|
||||
329 1 89 98
|
||||
330 1 89 99
|
||||
331 1 89 100
|
||||
332 1 90 99
|
||||
333 1 90 100
|
||||
334 1 91 92
|
||||
335 1 92 93
|
||||
336 1 93 94
|
||||
337 1 94 95
|
||||
338 1 95 96
|
||||
339 1 96 97
|
||||
340 1 97 98
|
||||
341 1 98 99
|
||||
342 1 99 100
|
||||
102
examples/rheo/oxidation/in.rheo.oxidation
Normal file
102
examples/rheo/oxidation/in.rheo.oxidation
Normal file
@ -0,0 +1,102 @@
|
||||
# ------ 2D oxidizing bar ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -60 60 0 80 -0.01 0.01 units box
|
||||
create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
|
||||
region lbar block -15 0 3 80 EDGE EDGE units box
|
||||
region rbar block 0 15 3 80 EDGE EDGE units box
|
||||
region bar union 2 lbar rbar
|
||||
region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
|
||||
|
||||
lattice hex 1.0
|
||||
create_atoms 1 region bar
|
||||
create_atoms 3 region floor
|
||||
|
||||
set region rbar type 2
|
||||
group bar type 1 2
|
||||
group rbar type 2
|
||||
group floor type 3
|
||||
|
||||
set group all sph/e 0.0
|
||||
set group all rheo/status 1
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.1*${rho0}/${mp}
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 0.1
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
create_bonds many bar bar 1 0 1.5
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style hybrid bpm/spring rheo/shell t/form 100
|
||||
bond_coeff 1 bpm/spring 1.0 1.0 1.0
|
||||
bond_coeff 2 rheo/shell 0.2 0.2 0.1
|
||||
|
||||
# ------ Apply dynamics ------#
|
||||
|
||||
# Note: surface detection is not performed on solid bodies, so cannot use surface property
|
||||
compute coord all rheo/property/atom coordination
|
||||
variable surf atom c_coord<22
|
||||
group surf dynamic all var surf every 10
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 &
|
||||
thermal &
|
||||
shift &
|
||||
surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} &
|
||||
specific/heat * constant ${Cv} &
|
||||
Tfreeze * constant ${Tf} &
|
||||
latent/heat * constant ${L} &
|
||||
react 1.5 1
|
||||
|
||||
fix 5 rbar rheo/oxidation 1.5 2 1.0
|
||||
fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 7 all gravity 5e-5 vector 0 -1 0
|
||||
fix 8 floor setforce 0.0 0.0 0.0
|
||||
fix 9 surf add/heat linear 1.1 0.5
|
||||
fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
|
||||
fix 11 all enforce2d
|
||||
|
||||
compute surf all rheo/property/atom surface
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond_shell all rheo/property/atom nbond/shell
|
||||
compute nbond_solid all nbond/atom bond/type 1
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf
|
||||
|
||||
run 40000
|
||||
486
examples/rheo/oxidation/log.27Jun2024.oxidation.g++.4
Normal file
486
examples/rheo/oxidation/log.27Jun2024.oxidation.g++.4
Normal file
@ -0,0 +1,486 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
# ------ 2D oxidizing bar ------ #
|
||||
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style hybrid rheo/thermal bond
|
||||
boundary m m p
|
||||
comm_modify vel yes
|
||||
newton off
|
||||
|
||||
region box block -60 60 0 80 -0.01 0.01 units box
|
||||
create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
Created orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
region lbar block -15 0 3 80 EDGE EDGE units box
|
||||
region rbar block 0 15 3 80 EDGE EDGE units box
|
||||
region bar union 2 lbar rbar
|
||||
region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box
|
||||
|
||||
lattice hex 1.0
|
||||
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||
create_atoms 1 region bar
|
||||
Created 2255 atoms
|
||||
using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||
create_atoms CPU = 0.004 seconds
|
||||
create_atoms 3 region floor
|
||||
Created 446 atoms
|
||||
using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set region rbar type 2
|
||||
Setting atom values ...
|
||||
1148 settings made for type
|
||||
group bar type 1 2
|
||||
2255 atoms in group bar
|
||||
group rbar type 2
|
||||
1148 atoms in group rbar
|
||||
group floor type 3
|
||||
446 atoms in group floor
|
||||
|
||||
set group all sph/e 0.0
|
||||
Setting atom values ...
|
||||
2701 settings made for sph/e
|
||||
set group all rheo/status 1
|
||||
Setting atom values ...
|
||||
2701 settings made for rheo/status
|
||||
|
||||
# ------ Model parameters ------#
|
||||
|
||||
variable cut equal 3.0
|
||||
variable n equal 1.0
|
||||
variable rho0 equal 1.0
|
||||
variable cs equal 1.0
|
||||
variable mp equal ${rho0}/${n}
|
||||
variable mp equal 1/${n}
|
||||
variable mp equal 1/1
|
||||
variable zeta equal 0.05
|
||||
variable kappa equal 0.1*${rho0}/${mp}
|
||||
variable kappa equal 0.1*1/${mp}
|
||||
variable kappa equal 0.1*1/1
|
||||
variable dt_max equal 0.1*${cut}/${cs}/3
|
||||
variable dt_max equal 0.1*3/${cs}/3
|
||||
variable dt_max equal 0.1*3/1/3
|
||||
variable eta equal 0.05
|
||||
variable Cv equal 1.0
|
||||
variable L equal 0.1
|
||||
variable Tf equal 1.0
|
||||
|
||||
mass * ${mp}
|
||||
mass * 1
|
||||
timestep 0.1
|
||||
|
||||
pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
|
||||
pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
|
||||
pair_coeff * * rheo
|
||||
pair_coeff * * rheo/solid 1.0 1.0 1.0
|
||||
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
0 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
create_bonds many bar bar 1 0 1.5
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 73 49 1
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair rheo, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(3) pair rheo/solid, perpetual, trim from (2)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Added 6547 bonds, new total = 6547
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
6 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
bond_style hybrid bpm/spring rheo/shell t/form 100
|
||||
bond_coeff 1 bpm/spring 1.0 1.0 1.0
|
||||
bond_coeff 2 rheo/shell 0.2 0.2 0.1
|
||||
|
||||
# ------ Apply dynamics ------#
|
||||
|
||||
# Note: surface detection is not performed on solid bodies, so cannot use surface property
|
||||
compute coord all rheo/property/atom coordination
|
||||
variable surf atom c_coord<22
|
||||
group surf dynamic all var surf every 10
|
||||
dynamic group surf defined
|
||||
|
||||
fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8
|
||||
fix 2 all rheo/viscosity * constant ${eta}
|
||||
fix 2 all rheo/viscosity * constant 0.05
|
||||
fix 3 all rheo/pressure * linear
|
||||
fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1
|
||||
fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 0.1 react 1.5 1
|
||||
|
||||
fix 5 rbar rheo/oxidation 1.5 2 1.0
|
||||
fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
|
||||
fix 7 all gravity 5e-5 vector 0 -1 0
|
||||
fix 8 floor setforce 0.0 0.0 0.0
|
||||
fix 9 surf add/heat linear 1.1 0.5
|
||||
fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
|
||||
fix 11 all enforce2d
|
||||
|
||||
compute surf all rheo/property/atom surface
|
||||
compute rho all rheo/property/atom rho
|
||||
compute phase all rheo/property/atom phase
|
||||
compute temp all rheo/property/atom temperature
|
||||
compute eng all rheo/property/atom energy
|
||||
compute nbond_shell all rheo/property/atom nbond/shell
|
||||
compute nbond_solid all nbond/atom bond/type 1
|
||||
|
||||
# ------ Output & Run ------ #
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step time ke press atoms
|
||||
|
||||
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf
|
||||
|
||||
run 40000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- BPM bond style: doi:10.1039/D3SM01373A
|
||||
|
||||
@Article{Clemmer2024,
|
||||
author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
|
||||
title = {A soft departure from jamming: the compaction of deformable
|
||||
granular matter under high pressures},
|
||||
journal = {Soft Matter},
|
||||
year = 2024,
|
||||
volume = 20,
|
||||
number = 8,
|
||||
pages = {1702--1718}
|
||||
}
|
||||
|
||||
- @article{PalermoInPrep,
|
||||
journal = {in prep},
|
||||
title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
|
||||
year = {2024},
|
||||
author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
|
||||
}
|
||||
|
||||
- @article{ApplMathModel.130.310,
|
||||
title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
|
||||
journal = {Applied Mathematical Modelling},
|
||||
volume = {130},
|
||||
pages = {310-326},
|
||||
year = {2024},
|
||||
issn = {0307-904X},
|
||||
doi = {https://doi.org/10.1016/j.apm.2024.02.027},
|
||||
author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.3
|
||||
ghost atom cutoff = 3.3
|
||||
binsize = 1.65, bins = 73 49 1
|
||||
8 neighbor lists, perpetual/occasional/extra = 7 1 0
|
||||
(1) pair rheo, perpetual, half/full from (3)
|
||||
attributes: half, newton off
|
||||
pair build: halffull/newtoff
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair rheo/solid, perpetual, trim from (4)
|
||||
attributes: half, newton off, cut 1.3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute RHEO/KERNEL, perpetual
|
||||
attributes: full, newton off
|
||||
pair build: full/bin
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(4) compute RHEO/GRAD, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) compute RHEO/VSHIFT, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) compute RHEO/SURFACE, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(7) fix rheo/thermal, occasional, trim from (4)
|
||||
attributes: half, newton off, cut 3
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(8) fix rheo/oxidation, perpetual, trim from (3)
|
||||
attributes: full, newton off, cut 1.8
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 25.96 | 25.96 | 25.96 Mbytes
|
||||
Step Time KinEng Press Atoms
|
||||
0 0 0 0 2701
|
||||
200 20 4.1737457e-07 1.298459e-07 2701
|
||||
400 40 1.6692448e-06 4.9223021e-07 2701
|
||||
600 60 3.7115752e-06 1.0476692e-05 2701
|
||||
800 80 4.678922e-06 0.00015017477 2701
|
||||
1000 100 4.7534549e-06 0.00027967322 2701
|
||||
1200 120 3.4532974e-06 0.00045908503 2701
|
||||
1400 140 1.4159611e-06 0.00055855688 2701
|
||||
1600 160 4.5151976e-07 0.00058351591 2701
|
||||
1800 180 5.1656107e-07 0.00055163637 2701
|
||||
2000 200 1.882995e-06 0.00048349046 2701
|
||||
2200 220 3.3481991e-06 0.00037790487 2701
|
||||
2400 240 3.8173347e-06 0.00023972848 2701
|
||||
2600 260 3.1832818e-06 9.5696995e-05 2701
|
||||
2800 280 1.5994934e-06 -2.7484809e-05 2701
|
||||
3000 300 3.573403e-07 -8.56391e-05 2701
|
||||
3200 320 1.6485893e-07 -5.6974248e-05 2701
|
||||
3400 340 8.5665044e-07 3.473389e-06 2701
|
||||
3600 360 2.0801421e-06 5.7938582e-05 2701
|
||||
3800 380 3.1934959e-06 0.00016746888 2701
|
||||
4000 400 3.2540476e-06 0.00026471904 2701
|
||||
4200 420 2.5603544e-06 0.00037699521 2701
|
||||
4400 440 1.4309318e-06 0.00047456272 2701
|
||||
4600 460 6.5231009e-07 0.00050551979 2701
|
||||
4800 480 6.9010626e-07 0.00048100816 2701
|
||||
5000 500 1.2663499e-06 0.00042166061 2701
|
||||
5200 520 2.0653769e-06 0.00033547376 2701
|
||||
5400 540 2.2709253e-06 0.00023015884 2701
|
||||
5600 560 1.7864994e-06 0.00013378564 2701
|
||||
5800 580 9.5638493e-07 4.4666688e-05 2701
|
||||
6000 600 3.0331342e-07 -1.884252e-06 2701
|
||||
6200 620 3.451498e-07 8.3090163e-07 2701
|
||||
6400 640 9.5098597e-07 4.7759688e-05 2701
|
||||
6600 660 1.8169765e-06 0.00011801205 2701
|
||||
6800 680 2.3723951e-06 0.00019823562 2701
|
||||
7000 700 2.3542553e-06 0.00028873701 2701
|
||||
7200 720 1.9132157e-06 0.00036386547 2701
|
||||
7400 740 1.4123115e-06 0.00040731263 2701
|
||||
7600 760 1.2422941e-06 0.00041151319 2701
|
||||
7800 780 1.4355275e-06 0.00038364583 2701
|
||||
8000 800 1.7835754e-06 0.00032724239 2701
|
||||
8200 820 1.961321e-06 0.00025932051 2701
|
||||
8400 840 1.8005786e-06 0.00018763659 2701
|
||||
8600 860 1.4274768e-06 0.00012392727 2701
|
||||
8800 880 1.075959e-06 8.1241673e-05 2701
|
||||
9000 900 1.014674e-06 7.0104531e-05 2701
|
||||
9200 920 1.3155353e-06 8.7991534e-05 2701
|
||||
9400 940 1.815649e-06 0.00012975516 2701
|
||||
9600 960 2.2699387e-06 0.0001861001 2701
|
||||
9800 980 2.4916284e-06 0.00024375475 2701
|
||||
10000 1000 2.4741893e-06 0.00029466715 2701
|
||||
10200 1020 2.3835838e-06 0.00032733587 2701
|
||||
10400 1040 2.3816351e-06 0.00033659466 2701
|
||||
10600 1060 2.5177605e-06 0.00032136429 2701
|
||||
10800 1080 2.6973866e-06 0.00028678114 2701
|
||||
11000 1100 2.8219278e-06 0.00023889501 2701
|
||||
11200 1120 2.794743e-06 0.00019226876 2701
|
||||
11400 1140 2.667182e-06 0.00015100316 2701
|
||||
11600 1160 2.5918212e-06 0.00012484649 2701
|
||||
11800 1180 2.6802845e-06 0.00011912201 2701
|
||||
12000 1200 2.9620111e-06 0.00013336302 2701
|
||||
12200 1220 3.3281225e-06 0.00016262605 2701
|
||||
12400 1240 3.6587842e-06 0.00020175308 2701
|
||||
12600 1260 3.8696418e-06 0.00023984351 2701
|
||||
12800 1280 3.9774608e-06 0.00026981166 2701
|
||||
13000 1300 4.0621923e-06 0.00028706126 2701
|
||||
13200 1320 4.2118368e-06 0.00028639136 2701
|
||||
13400 1340 4.4229032e-06 0.00026844105 2701
|
||||
13600 1360 4.6415059e-06 0.00023789752 2701
|
||||
13800 1380 4.8106868e-06 0.00020524655 2701
|
||||
14000 1400 4.9343741e-06 0.00017392428 2701
|
||||
14200 1420 5.0835921e-06 0.00015013775 2701
|
||||
14400 1440 5.3365604e-06 0.0001413941 2701
|
||||
14600 1460 5.7248817e-06 0.00014521418 2701
|
||||
14800 1480 6.2145391e-06 0.00016109563 2701
|
||||
15000 1500 6.7347576e-06 0.00018481456 2701
|
||||
15200 1520 7.221694e-06 0.00020956545 2701
|
||||
15400 1540 7.6762698e-06 0.0002293694 2701
|
||||
15600 1560 8.1313425e-06 0.00024058679 2701
|
||||
15800 1580 8.6053324e-06 0.00024015877 2701
|
||||
16000 1600 9.1091988e-06 0.00022927412 2701
|
||||
16200 1620 9.6165964e-06 0.00021035982 2701
|
||||
16400 1640 1.0093906e-05 0.00018782673 2701
|
||||
16600 1660 1.0561165e-05 0.00016863993 2701
|
||||
16800 1680 1.1066274e-05 0.00015693261 2701
|
||||
17000 1700 1.1661861e-05 0.00015221008 2701
|
||||
17200 1720 1.236148e-05 0.00015781879 2701
|
||||
17400 1740 1.3124872e-05 0.00017008789 2701
|
||||
17600 1760 1.3924606e-05 0.00018628888 2701
|
||||
17800 1780 1.4733479e-05 0.0002011741 2701
|
||||
18000 1800 1.5558838e-05 0.00021115187 2701
|
||||
18200 1820 1.6415631e-05 0.00021314897 2701
|
||||
18400 1840 1.7287377e-05 0.00020793654 2701
|
||||
18600 1860 1.8202577e-05 0.00019550685 2701
|
||||
18800 1880 1.9126239e-05 0.00018102715 2701
|
||||
19000 1900 2.0074716e-05 0.0001684831 2701
|
||||
19200 1920 2.1090982e-05 0.00015956926 2701
|
||||
19400 1940 2.2180303e-05 0.00015805759 2701
|
||||
19600 1960 2.3330404e-05 0.00016157807 2701
|
||||
19800 1980 2.4557652e-05 0.00017047221 2701
|
||||
20000 2000 2.5841568e-05 0.00018216972 2701
|
||||
20200 2020 2.7188233e-05 0.00018953358 2701
|
||||
20400 2040 2.8576958e-05 0.00019304182 2701
|
||||
20600 2060 2.999218e-05 0.00019239757 2701
|
||||
20800 2080 3.1437794e-05 0.00018759619 2701
|
||||
21000 2100 3.2938831e-05 0.00017863274 2701
|
||||
21200 2120 3.4506515e-05 0.00016911647 2701
|
||||
21400 2140 3.6126713e-05 0.00016161126 2701
|
||||
21600 2160 3.7812343e-05 0.0001583968 2701
|
||||
21800 2180 3.9564996e-05 0.00016178647 2701
|
||||
22000 2200 4.1406387e-05 0.00016872633 2701
|
||||
22200 2220 4.3340255e-05 0.00017435061 2701
|
||||
22400 2240 4.5333317e-05 0.00017910049 2701
|
||||
22600 2260 4.7311785e-05 0.0001800877 2701
|
||||
22800 2280 4.9303605e-05 0.00017728464 2701
|
||||
23000 2300 5.1334424e-05 0.00017486007 2701
|
||||
23200 2320 5.3402091e-05 0.00016867905 2701
|
||||
23400 2340 5.5505853e-05 0.00016402807 2701
|
||||
23600 2360 5.7679415e-05 0.00016343865 2701
|
||||
23800 2380 5.9920078e-05 0.00016623374 2701
|
||||
24000 2400 6.2239328e-05 0.00017028032 2701
|
||||
24200 2420 6.4624902e-05 0.00017371561 2701
|
||||
24400 2440 6.7054046e-05 0.00017565916 2701
|
||||
24600 2460 6.9522453e-05 0.00017545566 2701
|
||||
24800 2480 7.2079202e-05 0.00017437049 2701
|
||||
25000 2500 7.4716585e-05 0.00017043497 2701
|
||||
25200 2520 7.7415627e-05 0.00016579093 2701
|
||||
25400 2540 8.0169507e-05 0.00016268419 2701
|
||||
25600 2560 8.3001779e-05 0.00016233687 2701
|
||||
25800 2580 8.5921287e-05 0.00016275719 2701
|
||||
26000 2600 8.8880908e-05 0.00016425339 2701
|
||||
26200 2620 9.1881788e-05 0.00016478504 2701
|
||||
26400 2640 9.4969348e-05 0.00016371806 2701
|
||||
26600 2660 9.817611e-05 0.00016339555 2701
|
||||
26800 2680 0.00010146396 0.00015937569 2701
|
||||
27000 2700 0.00010485972 0.0001562082 2701
|
||||
27200 2720 0.00010837565 0.00015181198 2701
|
||||
27400 2740 0.00011187666 0.00015162336 2701
|
||||
27600 2760 0.00011543324 0.0001606148 2701
|
||||
27800 2780 0.00011905739 0.00016161123 2701
|
||||
28000 2800 0.00012280117 0.00016267347 2701
|
||||
28200 2820 0.00012665753 0.00016393863 2701
|
||||
28400 2840 0.00013061568 0.00016168097 2701
|
||||
28600 2860 0.00013469542 0.00015439793 2701
|
||||
28800 2880 0.00013889392 0.00014870639 2701
|
||||
29000 2900 0.00014307887 0.00015020156 2701
|
||||
29200 2920 0.00014714875 0.00015727801 2701
|
||||
29400 2940 0.0001510796 0.00016230922 2701
|
||||
29600 2960 0.0001551489 0.00016725059 2701
|
||||
29800 2980 0.00015918695 0.0001556229 2701
|
||||
30000 3000 0.00016145717 0.00015704562 2701
|
||||
30200 3020 0.00016164704 0.00015902669 2701
|
||||
30400 3040 0.00016250791 0.00017587854 2701
|
||||
30600 3060 0.0001639094 0.00016958759 2701
|
||||
30800 3080 0.00016479103 0.00016810892 2701
|
||||
31000 3100 0.00016521873 0.00016027053 2701
|
||||
31200 3120 0.00016540216 0.00015397865 2701
|
||||
31400 3140 0.00016690063 0.00015955009 2701
|
||||
31600 3160 0.00016832002 0.00015593907 2701
|
||||
31800 3180 0.00016948949 0.00015690982 2701
|
||||
32000 3200 0.0001700061 0.00016199222 2701
|
||||
32200 3220 0.00017122936 0.00016220019 2701
|
||||
32400 3240 0.00017198531 0.00015194229 2701
|
||||
32600 3260 0.00017286097 0.00014880433 2701
|
||||
32800 3280 0.00017395847 0.00014887179 2701
|
||||
33000 3300 0.00017527125 0.00015338612 2701
|
||||
33200 3320 0.00017667877 0.00014965389 2701
|
||||
33400 3340 0.00017944144 0.00014195087 2701
|
||||
33600 3360 0.0001807053 0.00014509998 2701
|
||||
33800 3380 0.00018242869 0.00014683629 2701
|
||||
34000 3400 0.00018415985 0.00014295872 2701
|
||||
34200 3420 0.00018635902 0.00013823794 2701
|
||||
34400 3440 0.00018885401 0.00013629126 2701
|
||||
34600 3460 0.00019106836 0.000138816 2701
|
||||
34800 3480 0.00019256787 0.00014358744 2701
|
||||
35000 3500 0.00019410016 0.0001420669 2701
|
||||
35200 3520 0.00019563657 0.0001340349 2701
|
||||
35400 3540 0.00019734994 0.00012994197 2701
|
||||
35600 3560 0.00019880477 0.00013331695 2701
|
||||
35800 3580 0.00020014422 0.00013848097 2701
|
||||
36000 3600 0.00020165626 0.00013796434 2701
|
||||
36200 3620 0.00020297057 0.0001346407 2701
|
||||
36400 3640 0.00020432584 0.00012838525 2701
|
||||
36600 3660 0.00020530152 0.00012848442 2701
|
||||
36800 3680 0.00020709012 0.0001296875 2701
|
||||
37000 3700 0.00020939979 0.00017016832 2701
|
||||
37200 3720 0.00021026158 0.00017388254 2701
|
||||
37400 3740 0.00021203076 0.00012169741 2701
|
||||
37600 3760 0.00021407912 0.00012467048 2701
|
||||
37800 3780 0.00021652866 0.000129545 2701
|
||||
38000 3800 0.00021927979 0.00013537464 2701
|
||||
38200 3820 0.00022175274 0.00014124275 2701
|
||||
38400 3840 0.00022431717 0.0001456533 2701
|
||||
38600 3860 0.00022586947 0.00015646735 2701
|
||||
38800 3880 0.00021974508 0.0001467496 2701
|
||||
39000 3900 0.00021270891 0.0001291023 2701
|
||||
39200 3920 0.00020709839 0.00014468038 2701
|
||||
39400 3940 0.00020138943 0.000156103 2701
|
||||
39600 3960 0.00019579027 0.00015207179 2701
|
||||
39800 3980 0.00019219602 0.0001548601 2701
|
||||
40000 4000 0.00018931715 0.00013543387 2701
|
||||
Loop time of 169.513 on 4 procs for 40000 steps with 2701 atoms
|
||||
|
||||
Performance: 2038784.562 tau/day, 235.970 timesteps/s, 637.356 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 16.279 | 22.828 | 28 | 98.9 | 13.47
|
||||
Bond | 0.88503 | 1.4645 | 2.0916 | 36.3 | 0.86
|
||||
Neigh | 29.832 | 29.954 | 30.069 | 1.5 | 17.67
|
||||
Comm | 1.2274 | 1.3406 | 1.4623 | 7.3 | 0.79
|
||||
Output | 0.0041506 | 0.0054325 | 0.0062685 | 1.1 | 0.00
|
||||
Modify | 107.8 | 113.27 | 120.23 | 47.8 | 66.82
|
||||
Other | | 0.6549 | | | 0.39
|
||||
|
||||
Nlocal: 675.25 ave 1362 max 1 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 94.75 ave 154 max 45 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 10485 ave 21200 max 18 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 20408.5 ave 41306 max 18 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 81634
|
||||
Ave neighs/atom = 30.223621
|
||||
Ave special neighs/atom = 1.7304702
|
||||
Neighbor list builds = 39994
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:50
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user