Merge branch 'develop' into regression-tests
This commit is contained in:
Axel Kohlmeyer
@ -101,6 +101,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
|
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ADDSYM(extract_setting);
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||||
ADDSYM(extract_global_datatype);
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||||
ADDSYM(extract_global);
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ADDSYM(extract_pair_dimension);
|
||||
ADDSYM(extract_pair);
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ADDSYM(map_atom);
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||||
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||||
ADDSYM(extract_atom_datatype);
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||||
@ -148,6 +150,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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ADDSYM(config_has_png_support);
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ADDSYM(config_has_jpeg_support);
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ADDSYM(config_has_ffmpeg_support);
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ADDSYM(config_has_curl_support);
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ADDSYM(config_has_exceptions);
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ADDSYM(config_has_package);
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||||
@ -144,11 +144,13 @@ struct _liblammpsplugin {
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int (*get_mpi_comm)(void *);
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||||
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||||
int (*extract_setting)(void *, const char *);
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||||
int *(*extract_global_datatype)(void *, const char *);
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||||
int (*extract_global_datatype)(void *, const char *);
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||||
void *(*extract_global)(void *, const char *);
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void *(*map_atom)(void *, const void *);
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||||
int (*extract_pair_dimension)(void *, const char *);
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||||
void *(*extract_pair)(void *, const char *);
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||||
int (*map_atom)(void *, const void *);
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||||
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int *(*extract_atom_datatype)(void *, const char *);
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||||
int (*extract_atom_datatype)(void *, const char *);
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void *(*extract_atom)(void *, const char *);
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||||
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||||
void *(*extract_compute)(void *, const char *, int, int);
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||||
@ -201,6 +203,7 @@ struct _liblammpsplugin {
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||||
int (*config_has_png_support)();
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int (*config_has_jpeg_support)();
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||||
int (*config_has_ffmpeg_support)();
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||||
int (*config_has_curl_support)();
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||||
int (*config_has_exceptions)();
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||||
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||||
int (*config_has_package)(const char *);
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||||
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||||
@ -5,9 +5,9 @@ dimension 3
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||||
atom_style full
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processors * * 1
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||||
|
||||
pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long"
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||||
pair_style lj/spica/coul/long 15.0
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||||
bond_style harmonic
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||||
angle_style sdk # compatible with "spica"
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angle_style spica
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special_bonds lj/coul 0.0 0.0 1.0
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||||
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read_data data.sds.gz
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@ -1,629 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Solvated 5-mer peptide
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units real
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atom_style full
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||||
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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||||
angle_style charmm
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dihedral_style charmm
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||||
improper_style harmonic
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kspace_style pppm 0.0001
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||||
|
||||
read_data data.peptide
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||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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2004 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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||||
14 = max dihedrals/atom
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||||
scanning impropers ...
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||||
1 = max impropers/atom
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||||
reading bonds ...
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1365 bonds
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||||
reading angles ...
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786 angles
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reading dihedrals ...
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||||
207 dihedrals
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reading impropers ...
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||||
12 impropers
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4 = max # of 1-2 neighbors
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||||
7 = max # of 1-3 neighbors
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||||
14 = max # of 1-4 neighbors
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||||
18 = max # of special neighbors
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||||
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||||
neighbor 2.0 bin
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neigh_modify delay 5
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||||
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timestep 2.0
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group peptide type <= 12
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||||
84 atoms in group peptide
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group one id 2 4 5 6
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4 atoms in group one
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group two id 80 82 83 84
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4 atoms in group two
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group ref id 37
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1 atoms in group ref
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group colvar union one two ref
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9 atoms in group colvar
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||||
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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||||
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||||
shell "rm -f out*.colvars.*"
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fix 2 all colvars peptide.colvars
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||||
fix 2a ref setforce 0.0 0.0 0.0
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||||
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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||||
6 = # of size 3 clusters
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||||
3 = # of size 4 clusters
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640 = # of frozen angles
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||||
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||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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||||
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||||
thermo_style custom step temp etotal pe ke epair ebond f_2
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||||
thermo 10
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||||
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||||
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run 100
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PPPM initialization ...
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||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.268725
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||||
grid = 15 15 15
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stencil order = 5
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||||
estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 10648 3375
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Neighbor list info ...
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||||
update every 1 steps, delay 5 steps, check yes
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||||
max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 5 5 5
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||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
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||||
(1) pair lj/charmm/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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colvars: Creating proxy instance
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colvars: ----------------------------------------------------------------------
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colvars: Initializing the collective variables module, version 2018-11-16.
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colvars: Please cite Fiorin et al, Mol Phys 2013:
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colvars: https://doi.org/10.1080/00268976.2013.813594
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||||
colvars: in any publication based on this calculation.
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colvars: SMP parallelism is available.
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colvars: Using LAMMPS interface, version 2018-08-29.
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colvars: ----------------------------------------------------------------------
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||||
colvars: Reading new configuration from file "peptide.colvars":
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||||
colvars: # smp = on [default]
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||||
colvars: # colvarsTrajFrequency = 1
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||||
colvars: # colvarsRestartFrequency = 1000
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||||
colvars: # scriptedColvarForces = off [default]
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||||
colvars: # scriptingAfterBiases = off [default]
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||||
colvars: ----------------------------------------------------------------------
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||||
colvars: Initializing a new collective variable.
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||||
colvars: # name = "one"
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||||
colvars: Initializing a new "distance" component.
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||||
colvars: # name = "" [default]
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||||
colvars: # componentCoeff = 1 [default]
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||||
colvars: # componentExp = 1 [default]
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||||
colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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||||
colvars: # forceNoPBC = off [default]
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colvars: # scalable = on [default]
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colvars: Initializing atom group "group1".
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||||
colvars: # name = "" [default]
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colvars: # centerReference = off [default]
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||||
colvars: # rotateReference = off [default]
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||||
colvars: # atomsOfGroup = "" [default]
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||||
colvars: # indexGroup = "" [default]
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||||
colvars: # psfSegID = [default]
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||||
colvars: # atomsFile = "" [default]
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||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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||||
colvars: # enableForces = on [default]
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colvars: # enableFitGradients = on [default]
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
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colvars: Initializing atom group "group2".
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||||
colvars: # name = "" [default]
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||||
colvars: # centerReference = off [default]
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||||
colvars: # rotateReference = off [default]
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||||
colvars: # atomsOfGroup = "" [default]
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||||
colvars: # indexGroup = "" [default]
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||||
colvars: # psfSegID = [default]
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||||
colvars: # atomsFile = "" [default]
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||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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||||
colvars: # enableForces = on [default]
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||||
colvars: # enableFitGradients = on [default]
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||||
colvars: # printAtomIDs = off [default]
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colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
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||||
colvars: # oneSiteSystemForce = off [default]
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||||
colvars: # oneSiteTotalForce = off [default]
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||||
colvars: All components initialized.
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colvars: # timeStepFactor = 1 [default]
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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||||
colvars: # upperBoundary = 0 [default]
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||||
colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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||||
colvars: # outputValue = on [default]
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||||
colvars: # outputVelocity = off [default]
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||||
colvars: # outputTotalForce = off [default]
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||||
colvars: # outputAppliedForce = off [default]
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||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
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||||
colvars: # name = "two"
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||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
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||||
colvars: # componentExp = 1 [default]
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||||
colvars: # period = 0 [default]
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||||
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.
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||||
colvars: Initializing atom group "group2".
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||||
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
|
||||
35 1.00345149123742e+01 9.58097344406653e+00
|
||||
32 1.00812605992407e+01 9.56689852729789e+00
|
||||
33 1.00636482078211e+01 9.57008522470067e+00
|
||||
34 1.00481219532447e+01 9.57404682801176e+00
|
||||
35 1.00345149123742e+01 9.58097344406654e+00
|
||||
36 1.00224896192326e+01 9.59352147402459e+00
|
||||
37 1.00117065902086e+01 9.61412496221624e+00
|
||||
38 1.00019625883763e+01 9.64369256665448e+00
|
||||
39 9.99324045988116e+00 9.68100279483232e+00
|
||||
40 9.98566198277188e+00 9.72340741886406e+00
|
||||
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141 1.00644400705403e+01 9.95041823460627e+00
|
||||
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|
||||
143 1.00436834568360e+01 9.89050941892251e+00
|
||||
144 1.00330649755670e+01 9.85603943369589e+00
|
||||
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
|
||||
152 9.96598267372795e+00 9.59318709218540e+00
|
||||
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
|
||||
159 9.95942460236116e+00 9.52452561453112e+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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|
||||
199 1.00122066751424e+01 9.63383866285097e+00
|
||||
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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|
||||
241 1.00548770491533e+01 9.72611599020063e+00
|
||||
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|
||||
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|
||||
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|
||||
245 1.00788811512303e+01 9.69472082245661e+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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|
||||
295 1.00056261321876e+01 9.72399810930261e+00
|
||||
296 9.99406221883501e+00 9.74140402524052e+00
|
||||
297 9.98250803362175e+00 9.75776438941627e+00
|
||||
298 9.97160202027972e+00 9.77203069297329e+00
|
||||
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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|
||||
230 9.98078771543058e+00 9.93636510426670e+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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|
||||
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
|
||||
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|
||||
282 1.00522576689401e+01 9.60085551333600e+00
|
||||
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|
||||
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
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
|
||||
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
|
||||
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
|
||||
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
|
||||
@ -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
|
||||
|
||||
@ -1,6 +1,12 @@
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
# run the first part and write out restart
|
||||
include in.molecular-mix
|
||||
write_restart molecular-mix.restart
|
||||
|
||||
# now restart
|
||||
clear
|
||||
molecule cychex cyclohexane.mol
|
||||
read_restart molecular-mix.restart
|
||||
|
||||
@ -9,3 +15,6 @@ thermo 100
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
|
||||
# clean up
|
||||
shell rm molecular-mix.restart
|
||||
|
||||
@ -1,6 +1,12 @@
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
# run the first part and write out restart
|
||||
include in.template-mix
|
||||
write_restart template-mix.restart
|
||||
|
||||
# now restart
|
||||
clear
|
||||
molecule cychex cyclohexane.mol
|
||||
read_restart template-mix.restart
|
||||
|
||||
@ -9,3 +15,6 @@ thermo 100
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
|
||||
# clean up
|
||||
shell rm template-mix.restart
|
||||
|
||||
302
examples/template/log.12Aug24.mol-restart-mix.g++.1
Normal file
302
examples/template/log.12Aug24.mol-restart-mix.g++.1
Normal file
@ -0,0 +1,302 @@
|
||||
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
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
# run the first part and write out restart
|
||||
include in.molecular-mix
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
LAMMPS molecule file. Cyclohexane(UA)
|
||||
1 molecules
|
||||
0 fragments
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style molecular
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
Lattice spacing in x,y,z = 6 6 6
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
|
||||
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
Created 3072 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.004 seconds
|
||||
create_atoms 2 random 800 495437 box
|
||||
Created 800 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
Generated 1 of 1 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 = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.28 | 12.28 | 12.28 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
|
||||
100 0 -4351.8383 516.49891 -3835.3394 11635.037
|
||||
190 0 -6191.8196 457.61266 -5734.2069 4365.4279
|
||||
Loop time of 2.5667 on 1 procs for 190 steps with 3872 atoms
|
||||
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
43897850768892.8 -5729.17409504969 -5734.20694761353
|
||||
Force two-norm initial, final = 1.1080994e+15 72.745546
|
||||
Force max component initial, final = 4.6607099e+14 17.390179
|
||||
Final line search alpha, max atom move = 0.0041638487 0.072410076
|
||||
Iterations, force evaluations = 190 297
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.2379 | 2.2379 | 2.2379 | 0.0 | 87.19
|
||||
Bond | 0.070658 | 0.070658 | 0.070658 | 0.0 | 2.75
|
||||
Neigh | 0.21093 | 0.21093 | 0.21093 | 0.0 | 8.22
|
||||
Comm | 0.012111 | 0.012111 | 0.012111 | 0.0 | 0.47
|
||||
Output | 3.0458e-05 | 3.0458e-05 | 3.0458e-05 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.03504 | | | 1.37
|
||||
|
||||
Nlocal: 3872 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12122 ave 12122 max 12122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 774375 ave 774375 max 774375 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 774375
|
||||
Ave neighs/atom = 199.99354
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 100 -6191.8196 457.61266 -4580.3354 4842.371
|
||||
100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321
|
||||
200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619
|
||||
300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123
|
||||
400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393
|
||||
500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524
|
||||
600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889
|
||||
700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164
|
||||
800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503
|
||||
900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352
|
||||
1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354
|
||||
1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244
|
||||
1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439
|
||||
1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716
|
||||
1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061
|
||||
1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408
|
||||
1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728
|
||||
1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923
|
||||
1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241
|
||||
1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835
|
||||
2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701
|
||||
2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632
|
||||
2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546
|
||||
2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574
|
||||
2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435
|
||||
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
|
||||
Loop time of 17.2353 on 1 procs for 2500 steps with 3872 atoms
|
||||
|
||||
Performance: 12.532 ns/day, 1.915 hours/ns, 145.052 timesteps/s, 561.639 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 | 15.936 | 15.936 | 15.936 | 0.0 | 92.46
|
||||
Bond | 0.5636 | 0.5636 | 0.5636 | 0.0 | 3.27
|
||||
Neigh | 0.51213 | 0.51213 | 0.51213 | 0.0 | 2.97
|
||||
Comm | 0.098127 | 0.098127 | 0.098127 | 0.0 | 0.57
|
||||
Output | 0.00072478 | 0.00072478 | 0.00072478 | 0.0 | 0.00
|
||||
Modify | 0.10177 | 0.10177 | 0.10177 | 0.0 | 0.59
|
||||
Other | | 0.02248 | | | 0.13
|
||||
|
||||
Nlocal: 3872 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11821 ave 11821 max 11821 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 770416 ave 770416 max 770416 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 770416
|
||||
Ave neighs/atom = 198.97107
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
#write_data molecular-mix.data
|
||||
#write_restart molecular-mix.restart
|
||||
write_restart molecular-mix.restart
|
||||
System init for write_restart ...
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
# now restart
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
LAMMPS molecule file. Cyclohexane(UA)
|
||||
1 molecules
|
||||
0 fragments
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
read_restart molecular-mix.restart
|
||||
Reading restart file ...
|
||||
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
|
||||
restoring atom style molecular from restart
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style lj/cut from restart
|
||||
restoring bond style harmonic from restart
|
||||
restoring angle style harmonic from restart
|
||||
restoring dihedral style harmonic from restart
|
||||
3872 atoms
|
||||
3072 bonds
|
||||
3072 angles
|
||||
3072 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
7 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_restart CPU = 0.003 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.12 | 11.12 | 11.12 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
|
||||
2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357
|
||||
2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67
|
||||
2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997
|
||||
2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823
|
||||
3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636
|
||||
3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576
|
||||
3200 297.34385 -5017.986 1603.4388 16.419054 10451.2
|
||||
3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096
|
||||
3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599
|
||||
3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632
|
||||
3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222
|
||||
3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292
|
||||
3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524
|
||||
3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697
|
||||
4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793
|
||||
4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442
|
||||
4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116
|
||||
4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216
|
||||
4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253
|
||||
4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246
|
||||
Loop time of 13.288 on 1 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 13.004 ns/day, 1.846 hours/ns, 150.512 timesteps/s, 582.781 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 | 12.191 | 12.191 | 12.191 | 0.0 | 91.74
|
||||
Bond | 0.4224 | 0.4224 | 0.4224 | 0.0 | 3.18
|
||||
Neigh | 0.50894 | 0.50894 | 0.50894 | 0.0 | 3.83
|
||||
Comm | 0.07309 | 0.07309 | 0.07309 | 0.0 | 0.55
|
||||
Output | 0.00057158 | 0.00057158 | 0.00057158 | 0.0 | 0.00
|
||||
Modify | 0.077778 | 0.077778 | 0.077778 | 0.0 | 0.59
|
||||
Other | | 0.01451 | | | 0.11
|
||||
|
||||
Nlocal: 3872 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11685 ave 11685 max 11685 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 770346 ave 770346 max 770346 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 770346
|
||||
Ave neighs/atom = 198.953
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
|
||||
# clean up
|
||||
shell rm molecular-mix.restart
|
||||
Total wall time: 0:00:33
|
||||
303
examples/template/log.12Aug24.mol-restart-mix.g++.4
Normal file
303
examples/template/log.12Aug24.mol-restart-mix.g++.4
Normal file
@ -0,0 +1,303 @@
|
||||
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
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
# run the first part and write out restart
|
||||
include in.molecular-mix
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
LAMMPS molecule file. Cyclohexane(UA)
|
||||
1 molecules
|
||||
0 fragments
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style molecular
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
Lattice spacing in x,y,z = 6 6 6
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
|
||||
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
Created 3072 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
create_atoms 2 random 800 495437 box
|
||||
Created 800 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
Generated 1 of 1 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 = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.623 | 9.719 | 10.01 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
|
||||
100 0 -3410.6986 572.28283 -2838.4158 14603.831
|
||||
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
|
||||
204 0 -6137.0238 483.1464 -5653.8774 4952.4083
|
||||
Loop time of 0.719327 on 4 procs for 204 steps with 3872 atoms
|
||||
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
7.54300441078755e+16 -5648.75822666276 -5653.87742467986
|
||||
Force two-norm initial, final = 8.7430661e+18 74.636836
|
||||
Force max component initial, final = 4.1468626e+18 8.680078
|
||||
Final line search alpha, max atom move = 0.0032186724 0.027938327
|
||||
Iterations, force evaluations = 204 328
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.60273 | 0.60882 | 0.61181 | 0.5 | 84.64
|
||||
Bond | 0.018965 | 0.019154 | 0.019363 | 0.1 | 2.66
|
||||
Neigh | 0.054004 | 0.054008 | 0.054012 | 0.0 | 7.51
|
||||
Comm | 0.022945 | 0.026108 | 0.032071 | 2.2 | 3.63
|
||||
Output | 3.4085e-05 | 3.6968e-05 | 4.5055e-05 | 0.0 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0112 | | | 1.56
|
||||
|
||||
Nlocal: 968 ave 980 max 954 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 6630 ave 6644 max 6616 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 193550 ave 195957 max 191376 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 774200
|
||||
Ave neighs/atom = 199.94835
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.498 | 8.785 | 8.881 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 100 -6137.0238 483.1464 -4500.0059 5429.3515
|
||||
100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922
|
||||
200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576
|
||||
300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841
|
||||
400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7
|
||||
500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519
|
||||
600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312
|
||||
700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062
|
||||
800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319
|
||||
900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218
|
||||
1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317
|
||||
1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434
|
||||
1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625
|
||||
1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169
|
||||
1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496
|
||||
1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052
|
||||
1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28
|
||||
1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096
|
||||
1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864
|
||||
1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513
|
||||
2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674
|
||||
2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49
|
||||
2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961
|
||||
2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853
|
||||
2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501
|
||||
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
|
||||
Loop time of 4.32954 on 4 procs for 2500 steps with 3872 atoms
|
||||
|
||||
Performance: 49.890 ns/day, 0.481 hours/ns, 577.429 timesteps/s, 2.236 Matom-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 | 3.8113 | 3.8529 | 3.8893 | 1.7 | 88.99
|
||||
Bond | 0.13153 | 0.13433 | 0.13718 | 0.7 | 3.10
|
||||
Neigh | 0.13036 | 0.13039 | 0.13042 | 0.0 | 3.01
|
||||
Comm | 0.13688 | 0.1751 | 0.21857 | 8.4 | 4.04
|
||||
Output | 0.00032606 | 0.00035873 | 0.00045009 | 0.0 | 0.01
|
||||
Modify | 0.027754 | 0.028116 | 0.028735 | 0.2 | 0.65
|
||||
Other | | 0.008382 | | | 0.19
|
||||
|
||||
Nlocal: 968 ave 986 max 944 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Nghost: 6379.75 ave 6407 max 6352 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 192584 ave 196718 max 188693 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 770338
|
||||
Ave neighs/atom = 198.95093
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
#write_data molecular-mix.data
|
||||
#write_restart molecular-mix.restart
|
||||
write_restart molecular-mix.restart
|
||||
System init for write_restart ...
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
# now restart
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
LAMMPS molecule file. Cyclohexane(UA)
|
||||
1 molecules
|
||||
0 fragments
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
read_restart molecular-mix.restart
|
||||
Reading restart file ...
|
||||
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
|
||||
restoring atom style molecular from restart
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cut from restart
|
||||
restoring bond style harmonic from restart
|
||||
restoring angle style harmonic from restart
|
||||
restoring dihedral style harmonic from restart
|
||||
3872 atoms
|
||||
3072 bonds
|
||||
3072 angles
|
||||
3072 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
7 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_restart CPU = 0.004 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.475 | 8.571 | 8.857 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
|
||||
2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533
|
||||
2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127
|
||||
2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494
|
||||
2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3
|
||||
3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459
|
||||
3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057
|
||||
3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933
|
||||
3300 297.45744 -4923.6217 1700.537 209.19205 8189.571
|
||||
3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119
|
||||
3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067
|
||||
3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481
|
||||
3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479
|
||||
3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521
|
||||
3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37
|
||||
4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386
|
||||
4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733
|
||||
4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158
|
||||
4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862
|
||||
4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975
|
||||
4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294
|
||||
Loop time of 3.58588 on 4 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 48.189 ns/day, 0.498 hours/ns, 557.743 timesteps/s, 2.160 Matom-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 | 3.0873 | 3.1383 | 3.2136 | 2.7 | 87.52
|
||||
Bond | 0.10381 | 0.10769 | 0.11168 | 0.9 | 3.00
|
||||
Neigh | 0.13651 | 0.13652 | 0.13654 | 0.0 | 3.81
|
||||
Comm | 0.094882 | 0.1741 | 0.22894 | 12.3 | 4.86
|
||||
Output | 0.00024683 | 0.00028387 | 0.00038642 | 0.0 | 0.01
|
||||
Modify | 0.021974 | 0.022331 | 0.022623 | 0.2 | 0.62
|
||||
Other | | 0.006685 | | | 0.19
|
||||
|
||||
Nlocal: 968 ave 984 max 948 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 6349.5 ave 6370 max 6330 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 192457 ave 196654 max 187154 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 769828
|
||||
Ave neighs/atom = 198.81921
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
|
||||
# clean up
|
||||
shell rm molecular-mix.restart
|
||||
Total wall time: 0:00:08
|
||||
295
examples/template/log.12Aug24.tmpl-restart-mix.g++.1
Normal file
295
examples/template/log.12Aug24.tmpl-restart-mix.g++.1
Normal file
@ -0,0 +1,295 @@
|
||||
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
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
# run the first part and write out restart
|
||||
include in.template-mix
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 1: creating system with create_atoms
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
LAMMPS molecule file. Cyclohexane(UA)
|
||||
1 molecules
|
||||
0 fragments
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style template cychex
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
Lattice spacing in x,y,z = 6 6 6
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
|
||||
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
Created 3072 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 random 800 495437 box
|
||||
Created 800 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
Generated 1 of 1 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 = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.05 | 8.05 | 8.05 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
|
||||
100 0 -4351.8383 516.49891 -3835.3394 11635.037
|
||||
190 0 -6191.8196 457.61266 -5734.2069 4365.4279
|
||||
Loop time of 2.46574 on 1 procs for 190 steps with 3872 atoms
|
||||
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
43897850768892.8 -5729.17409504969 -5734.20694761353
|
||||
Force two-norm initial, final = 1.1080994e+15 72.745546
|
||||
Force max component initial, final = 4.6607099e+14 17.390179
|
||||
Final line search alpha, max atom move = 0.0041638487 0.072410076
|
||||
Iterations, force evaluations = 190 297
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1376 | 2.1376 | 2.1376 | 0.0 | 86.69
|
||||
Bond | 0.068456 | 0.068456 | 0.068456 | 0.0 | 2.78
|
||||
Neigh | 0.21212 | 0.21212 | 0.21212 | 0.0 | 8.60
|
||||
Comm | 0.012436 | 0.012436 | 0.012436 | 0.0 | 0.50
|
||||
Output | 2.9907e-05 | 2.9907e-05 | 2.9907e-05 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.03511 | | | 1.42
|
||||
|
||||
Nlocal: 3872 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12122 ave 12122 max 12122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 774375 ave 774375 max 774375 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 774375
|
||||
Ave neighs/atom = 199.99354
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.925 | 6.925 | 6.925 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 100 -6191.8196 457.61266 -4580.3354 4842.371
|
||||
100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321
|
||||
200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619
|
||||
300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123
|
||||
400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393
|
||||
500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524
|
||||
600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889
|
||||
700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164
|
||||
800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503
|
||||
900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352
|
||||
1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354
|
||||
1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244
|
||||
1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439
|
||||
1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716
|
||||
1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061
|
||||
1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408
|
||||
1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728
|
||||
1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923
|
||||
1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241
|
||||
1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835
|
||||
2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701
|
||||
2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632
|
||||
2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546
|
||||
2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574
|
||||
2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435
|
||||
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
|
||||
Loop time of 16.1773 on 1 procs for 2500 steps with 3872 atoms
|
||||
|
||||
Performance: 13.352 ns/day, 1.797 hours/ns, 154.537 timesteps/s, 598.368 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 | 14.927 | 14.927 | 14.927 | 0.0 | 92.27
|
||||
Bond | 0.52161 | 0.52161 | 0.52161 | 0.0 | 3.22
|
||||
Neigh | 0.52299 | 0.52299 | 0.52299 | 0.0 | 3.23
|
||||
Comm | 0.090871 | 0.090871 | 0.090871 | 0.0 | 0.56
|
||||
Output | 0.00059782 | 0.00059782 | 0.00059782 | 0.0 | 0.00
|
||||
Modify | 0.096104 | 0.096104 | 0.096104 | 0.0 | 0.59
|
||||
Other | | 0.01791 | | | 0.11
|
||||
|
||||
Nlocal: 3872 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11821 ave 11821 max 11821 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 770416 ave 770416 max 770416 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 770416
|
||||
Ave neighs/atom = 198.97107
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
#write_data template-mix.data
|
||||
#write_restart template-mix.restart
|
||||
write_restart template-mix.restart
|
||||
System init for write_restart ...
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
# now restart
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
LAMMPS molecule file. Cyclohexane(UA)
|
||||
1 molecules
|
||||
0 fragments
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
read_restart template-mix.restart
|
||||
Reading restart file ...
|
||||
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
|
||||
restoring atom style template from restart
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style lj/cut from restart
|
||||
restoring bond style harmonic from restart
|
||||
restoring angle style harmonic from restart
|
||||
restoring dihedral style harmonic from restart
|
||||
3872 atoms
|
||||
3072 template bonds
|
||||
3072 template angles
|
||||
3072 template dihedrals
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
|
||||
2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357
|
||||
2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67
|
||||
2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997
|
||||
2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823
|
||||
3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636
|
||||
3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576
|
||||
3200 297.34385 -5017.986 1603.4388 16.419054 10451.2
|
||||
3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096
|
||||
3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599
|
||||
3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632
|
||||
3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222
|
||||
3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292
|
||||
3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524
|
||||
3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697
|
||||
4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793
|
||||
4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442
|
||||
4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116
|
||||
4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216
|
||||
4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253
|
||||
4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246
|
||||
Loop time of 13.2399 on 1 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 13.051 ns/day, 1.839 hours/ns, 151.058 timesteps/s, 584.898 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 | 12.13 | 12.13 | 12.13 | 0.0 | 91.61
|
||||
Bond | 0.42044 | 0.42044 | 0.42044 | 0.0 | 3.18
|
||||
Neigh | 0.52469 | 0.52469 | 0.52469 | 0.0 | 3.96
|
||||
Comm | 0.072857 | 0.072857 | 0.072857 | 0.0 | 0.55
|
||||
Output | 0.00053188 | 0.00053188 | 0.00053188 | 0.0 | 0.00
|
||||
Modify | 0.076918 | 0.076918 | 0.076918 | 0.0 | 0.58
|
||||
Other | | 0.0148 | | | 0.11
|
||||
|
||||
Nlocal: 3872 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11685 ave 11685 max 11685 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 770346 ave 770346 max 770346 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 770346
|
||||
Ave neighs/atom = 198.953
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
|
||||
# clean up
|
||||
shell rm template-mix.restart
|
||||
Total wall time: 0:00:31
|
||||
296
examples/template/log.12Aug24.tmpl-restart-mix.g++.4
Normal file
296
examples/template/log.12Aug24.tmpl-restart-mix.g++.4
Normal file
@ -0,0 +1,296 @@
|
||||
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
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
# run the first part and write out restart
|
||||
include in.template-mix
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 1: creating system with create_atoms
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
LAMMPS molecule file. Cyclohexane(UA)
|
||||
1 molecules
|
||||
0 fragments
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style template cychex
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
Lattice spacing in x,y,z = 6 6 6
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
|
||||
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
Created 3072 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 2 random 800 495437 box
|
||||
Created 800 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
Generated 1 of 1 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 = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.345 | 5.441 | 5.728 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
|
||||
100 0 -3410.6986 572.28283 -2838.4158 14603.831
|
||||
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
|
||||
204 0 -6137.0238 483.1464 -5653.8774 4952.4083
|
||||
Loop time of 0.719475 on 4 procs for 204 steps with 3872 atoms
|
||||
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
7.54300441078755e+16 -5648.75822666276 -5653.87742467986
|
||||
Force two-norm initial, final = 8.7430661e+18 74.636836
|
||||
Force max component initial, final = 4.1468626e+18 8.680078
|
||||
Final line search alpha, max atom move = 0.0032186724 0.027938327
|
||||
Iterations, force evaluations = 204 328
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.59281 | 0.6027 | 0.60956 | 0.8 | 83.77
|
||||
Bond | 0.018776 | 0.020785 | 0.026388 | 2.2 | 2.89
|
||||
Neigh | 0.054209 | 0.054242 | 0.054273 | 0.0 | 7.54
|
||||
Comm | 0.018189 | 0.03064 | 0.042206 | 4.9 | 4.26
|
||||
Output | 3.3034e-05 | 3.5624e-05 | 4.3263e-05 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01107 | | | 1.54
|
||||
|
||||
Nlocal: 968 ave 980 max 954 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 6630 ave 6644 max 6616 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 193550 ave 195957 max 191376 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 774200
|
||||
Ave neighs/atom = 199.94835
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.22 | 4.507 | 4.603 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 100 -6137.0238 483.1464 -4500.0059 5429.3515
|
||||
100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922
|
||||
200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576
|
||||
300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841
|
||||
400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7
|
||||
500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519
|
||||
600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312
|
||||
700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062
|
||||
800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319
|
||||
900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218
|
||||
1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317
|
||||
1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434
|
||||
1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625
|
||||
1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169
|
||||
1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496
|
||||
1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052
|
||||
1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28
|
||||
1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096
|
||||
1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864
|
||||
1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513
|
||||
2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674
|
||||
2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49
|
||||
2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961
|
||||
2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853
|
||||
2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501
|
||||
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
|
||||
Loop time of 4.32742 on 4 procs for 2500 steps with 3872 atoms
|
||||
|
||||
Performance: 49.914 ns/day, 0.481 hours/ns, 577.711 timesteps/s, 2.237 Matom-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 | 3.7864 | 3.836 | 3.8948 | 2.2 | 88.64
|
||||
Bond | 0.13058 | 0.13362 | 0.13735 | 0.8 | 3.09
|
||||
Neigh | 0.13597 | 0.13601 | 0.13605 | 0.0 | 3.14
|
||||
Comm | 0.12304 | 0.18542 | 0.23763 | 10.5 | 4.28
|
||||
Output | 0.00033524 | 0.00036705 | 0.00045513 | 0.0 | 0.01
|
||||
Modify | 0.027504 | 0.027917 | 0.028571 | 0.3 | 0.65
|
||||
Other | | 0.008118 | | | 0.19
|
||||
|
||||
Nlocal: 968 ave 986 max 944 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Nghost: 6379.75 ave 6407 max 6352 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 192584 ave 196718 max 188693 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 770338
|
||||
Ave neighs/atom = 198.95093
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
#write_data template-mix.data
|
||||
#write_restart template-mix.restart
|
||||
write_restart template-mix.restart
|
||||
System init for write_restart ...
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
|
||||
# now restart
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
LAMMPS molecule file. Cyclohexane(UA)
|
||||
1 molecules
|
||||
0 fragments
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
read_restart template-mix.restart
|
||||
Reading restart file ...
|
||||
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
|
||||
restoring atom style template from restart
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cut from restart
|
||||
restoring bond style harmonic from restart
|
||||
restoring angle style harmonic from restart
|
||||
restoring dihedral style harmonic from restart
|
||||
3872 atoms
|
||||
3072 template bonds
|
||||
3072 template angles
|
||||
3072 template dihedrals
|
||||
read_restart CPU = 0.001 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.192 | 4.288 | 4.574 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
|
||||
2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533
|
||||
2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127
|
||||
2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494
|
||||
2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3
|
||||
3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459
|
||||
3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057
|
||||
3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933
|
||||
3300 297.45744 -4923.6217 1700.537 209.19205 8189.571
|
||||
3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119
|
||||
3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067
|
||||
3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481
|
||||
3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479
|
||||
3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521
|
||||
3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37
|
||||
4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386
|
||||
4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733
|
||||
4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158
|
||||
4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862
|
||||
4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975
|
||||
4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294
|
||||
Loop time of 3.5798 on 4 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 48.271 ns/day, 0.497 hours/ns, 558.691 timesteps/s, 2.163 Matom-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 | 3.0514 | 3.1162 | 3.2058 | 3.3 | 87.05
|
||||
Bond | 0.10377 | 0.10776 | 0.11194 | 1.0 | 3.01
|
||||
Neigh | 0.14121 | 0.14125 | 0.1413 | 0.0 | 3.95
|
||||
Comm | 0.092144 | 0.18542 | 0.25437 | 14.1 | 5.18
|
||||
Output | 0.00025632 | 0.00028151 | 0.00035298 | 0.0 | 0.01
|
||||
Modify | 0.02193 | 0.022227 | 0.022584 | 0.2 | 0.62
|
||||
Other | | 0.006618 | | | 0.18
|
||||
|
||||
Nlocal: 968 ave 984 max 948 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 6349.5 ave 6370 max 6330 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 192457 ave 196654 max 187154 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 769828
|
||||
Ave neighs/atom = 198.81921
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
|
||||
# clean up
|
||||
shell rm template-mix.restart
|
||||
Total wall time: 0:00:08
|
||||
@ -1,106 +0,0 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
read_restart molecular-mix.restart
|
||||
Reading restart file ...
|
||||
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
|
||||
restoring atom style molecular from restart
|
||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style lj/cut from restart
|
||||
restoring bond style harmonic from restart
|
||||
restoring angle style harmonic from restart
|
||||
restoring dihedral style harmonic from restart
|
||||
3872 atoms
|
||||
3072 bonds
|
||||
3072 angles
|
||||
3072 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
5 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_restart CPU = 0.008 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.74 | 10.74 | 10.74 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
||||
100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
|
||||
200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
|
||||
300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
|
||||
400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
|
||||
500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
|
||||
600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
|
||||
700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
|
||||
800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
|
||||
900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
|
||||
1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
|
||||
1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
|
||||
1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
|
||||
1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
|
||||
1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
|
||||
1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
|
||||
1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
|
||||
1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
|
||||
1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
|
||||
1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
|
||||
2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
|
||||
Loop time of 15.5879 on 1 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 11.086 ns/day, 2.165 hours/ns, 128.305 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 14.116 | 14.116 | 14.116 | 0.0 | 90.56
|
||||
Bond | 0.58742 | 0.58742 | 0.58742 | 0.0 | 3.77
|
||||
Neigh | 0.68543 | 0.68543 | 0.68543 | 0.0 | 4.40
|
||||
Comm | 0.082574 | 0.082574 | 0.082574 | 0.0 | 0.53
|
||||
Output | 0.00054698 | 0.00054698 | 0.00054698 | 0.0 | 0.00
|
||||
Modify | 0.078446 | 0.078446 | 0.078446 | 0.0 | 0.50
|
||||
Other | | 0.03761 | | | 0.24
|
||||
|
||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11633.0 ave 11633 max 11633 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 770365.0 ave 770365 max 770365 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 770365
|
||||
Ave neighs/atom = 198.95790
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:15
|
||||
@ -1,107 +0,0 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
read_restart molecular-mix.restart
|
||||
Reading restart file ...
|
||||
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
|
||||
WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:697)
|
||||
restoring atom style molecular from restart
|
||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cut from restart
|
||||
restoring bond style harmonic from restart
|
||||
restoring angle style harmonic from restart
|
||||
restoring dihedral style harmonic from restart
|
||||
3872 atoms
|
||||
3072 bonds
|
||||
3072 angles
|
||||
3072 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
5 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_restart CPU = 0.031 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.101 | 8.197 | 8.483 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
||||
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
|
||||
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
|
||||
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
|
||||
400 302 -4951.4895 1664.5419 197.74463 10784.638
|
||||
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
|
||||
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
|
||||
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
|
||||
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
|
||||
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
|
||||
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
|
||||
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
|
||||
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
|
||||
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
|
||||
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
|
||||
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
|
||||
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
|
||||
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
|
||||
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
|
||||
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
|
||||
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
|
||||
Loop time of 5.2142 on 4 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 33.140 ns/day, 0.724 hours/ns, 383.568 timesteps/s
|
||||
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.5706 | 3.6724 | 3.7809 | 4.9 | 70.43
|
||||
Bond | 0.14654 | 0.1524 | 0.15708 | 1.2 | 2.92
|
||||
Neigh | 0.18217 | 0.1822 | 0.18221 | 0.0 | 3.49
|
||||
Comm | 0.74346 | 0.8715 | 0.9808 | 10.9 | 16.71
|
||||
Output | 0.00034776 | 0.00084716 | 0.0023413 | 0.0 | 0.02
|
||||
Modify | 0.12457 | 0.18985 | 0.31013 | 17.4 | 3.64
|
||||
Other | | 0.145 | | | 2.78
|
||||
|
||||
Nlocal: 968.000 ave 979 max 948 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 6321.25 ave 6336 max 6309 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 192540.0 ave 195406 max 187182 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 770161
|
||||
Ave neighs/atom = 198.90522
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
@ -1,102 +0,0 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
read_restart template-mix.restart
|
||||
Reading restart file ...
|
||||
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
|
||||
WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:697)
|
||||
restoring atom style template from restart
|
||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
restoring pair style lj/cut from restart
|
||||
restoring bond style harmonic from restart
|
||||
restoring angle style harmonic from restart
|
||||
restoring dihedral style harmonic from restart
|
||||
3872 atoms
|
||||
3072 template bonds
|
||||
3072 template angles
|
||||
3072 template dihedrals
|
||||
read_restart CPU = 0.002 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.879 | 6.879 | 6.879 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
||||
2600 303.69861 -4872.1658 1620.5986 252.72467 8824.1501
|
||||
2700 304.64827 -4885.5903 1747.1956 376.85504 11560.748
|
||||
2800 298.79617 -4851.2752 1644.5913 241.04014 9198.1133
|
||||
2900 302.323 -4949.4247 1661.0637 200.05824 10788.039
|
||||
3000 302.8192 -4983.7441 1617.1412 127.5418 9606.2027
|
||||
3100 305.27495 -4999.5335 1589.7081 112.65547 9258.8096
|
||||
3200 294.9932 -4960.8253 1650.5396 93.556955 11103.25
|
||||
3300 299.8705 -4896.6757 1711.6029 275.0477 8404.2758
|
||||
3400 308.43113 -5035.583 1732.7837 256.09989 11520.651
|
||||
3500 302.54 -4887.2016 1770.4336 374.15506 8359.8351
|
||||
3600 294.00064 -5011.409 1768.0298 149.01058 11257.53
|
||||
3700 303.26654 -4942.0636 1690.4493 247.69209 8749.4281
|
||||
3800 294.7064 -5009.5839 1638.6276 29.577045 10460.396
|
||||
3900 300.34826 -5011.778 1699.4384 153.29355 9558.3891
|
||||
4000 298.76709 -5014.8089 1613.1902 45.769836 9254.1067
|
||||
4100 297.77294 -4978.3228 1736.8967 194.49122 10810.757
|
||||
4200 302.14768 -5049.4356 1713.0187 149.97929 8258.5093
|
||||
4300 295.1467 -5094.2287 1757.8215 69.206733 11022.023
|
||||
4400 305.24677 -4967.1951 1762.3252 317.28577 8423.2256
|
||||
4500 305.53119 -5047.7285 1775.2795 252.98852 11178.338
|
||||
Loop time of 15.3536 on 1 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 11.255 ns/day, 2.132 hours/ns, 130.263 timesteps/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 | 13.88 | 13.88 | 13.88 | 0.0 | 90.40
|
||||
Bond | 0.58065 | 0.58065 | 0.58065 | 0.0 | 3.78
|
||||
Neigh | 0.69518 | 0.69518 | 0.69518 | 0.0 | 4.53
|
||||
Comm | 0.0826 | 0.0826 | 0.0826 | 0.0 | 0.54
|
||||
Output | 0.00053438 | 0.00053438 | 0.00053438 | 0.0 | 0.00
|
||||
Modify | 0.07779 | 0.07779 | 0.07779 | 0.0 | 0.51
|
||||
Other | | 0.03687 | | | 0.24
|
||||
|
||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11670.0 ave 11670 max 11670 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 770032.0 ave 770032 max 770032 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 770032
|
||||
Ave neighs/atom = 198.87190
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:15
|
||||
@ -1,101 +0,0 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 3: continuing from restart file
|
||||
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
read_restart template-mix.restart
|
||||
Reading restart file ...
|
||||
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
|
||||
restoring atom style template from restart
|
||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
restoring pair style lj/cut from restart
|
||||
restoring bond style harmonic from restart
|
||||
restoring angle style harmonic from restart
|
||||
restoring dihedral style harmonic from restart
|
||||
3872 atoms
|
||||
3072 template bonds
|
||||
3072 template angles
|
||||
3072 template dihedrals
|
||||
read_restart CPU = 0.006 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
Resetting global fix info from restart file:
|
||||
fix style: nvt, fix ID: 1
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
All restart file global fix info was re-assigned
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.193 | 4.289 | 4.575 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
||||
2600 303.6986 -4872.1658 1620.5986 252.72458 8824.1501
|
||||
2700 296.80713 -4884.3012 1753.5243 293.99628 11523.482
|
||||
2800 298.88856 -4849.1995 1639.5709 239.1615 9214.1261
|
||||
2900 297.12578 -4949.9958 1657.7582 136.2123 10727.69
|
||||
3000 298.19234 -4984.9797 1618.0356 73.812582 9576.9074
|
||||
3100 301.54182 -4999.9775 1588.997 68.424766 9225.9502
|
||||
3200 294.07259 -4962.8351 1646.3012 76.686125 11080.923
|
||||
3300 303.55697 -4900.0696 1721.4077 323.99573 8433.7992
|
||||
3400 297.80636 -5036.3758 1735.0734 135.00054 11440.101
|
||||
3500 303.96121 -4882.4297 1757.4268 382.31908 8497.7685
|
||||
3600 298.21153 -5006.6599 1759.9584 194.27658 11184.938
|
||||
3700 300.77921 -4941.495 1688.3988 217.50964 8820.5666
|
||||
3800 294.33206 -5011.7746 1653.7511 38.190478 10418.208
|
||||
3900 304.38175 -5004.4071 1719.9139 227.68132 9632.0557
|
||||
4000 302.44152 -5029.0544 1610.1577 70.889929 9237.6379
|
||||
4100 298.82638 -4971.4109 1755.8272 232.48883 10814.056
|
||||
4200 297.77273 -5040.0028 1718.5112 114.42322 8287.605
|
||||
4300 300.50984 -5082.4128 1742.354 127.43881 11003.298
|
||||
4400 310.02885 -4971.4191 1749.1209 355.03646 8502.7004
|
||||
4500 302.62639 -5033.3284 1753.488 212.07956 11150.514
|
||||
Loop time of 4.39645 on 4 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 39.304 ns/day, 0.611 hours/ns, 454.913 timesteps/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.6185 | 3.6709 | 3.7028 | 1.7 | 83.50
|
||||
Bond | 0.14772 | 0.15338 | 0.1621 | 1.5 | 3.49
|
||||
Neigh | 0.17739 | 0.17747 | 0.17756 | 0.0 | 4.04
|
||||
Comm | 0.29637 | 0.33265 | 0.39131 | 6.7 | 7.57
|
||||
Output | 0.00034028 | 0.0006627 | 0.0016284 | 0.0 | 0.02
|
||||
Modify | 0.039076 | 0.041988 | 0.043469 | 0.9 | 0.96
|
||||
Other | | 0.01937 | | | 0.44
|
||||
|
||||
Nlocal: 968.000 ave 977 max 956 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Nghost: 6322.75 ave 6345 max 6308 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 192555.0 ave 195249 max 188636 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 770221
|
||||
Ave neighs/atom = 198.92071
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
Reference in New Issue
Block a user