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Merge branch 'develop' into apip_devel and solve merge conflict in set.

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This commit is contained in:
David Immel
2025-06-06 13:32:00 +02:00
parent e5f0e23a11 b3f160c118
commit 9a65ab2c4d
548 changed files with 50015 additions and 7438 deletions
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5
examples/COUPLE/plugin/CMakeLists.txt
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@ -27,10 +27,7 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
find_package(MPI REQUIRED)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI REQUIRED COMPONENTS C)
##########################

1
examples/COUPLE/plugin/liblammpsplugin.c
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@ -144,6 +144,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(find_pair_neighlist);
ADDSYM(find_fix_neighlist);
ADDSYM(find_compute_neighlist);
ADDSYM(request_single_neighlist);
ADDSYM(neighlist_num_elements);
ADDSYM(neighlist_element_neighbors);

18
examples/COUPLE/plugin/liblammpsplugin.h
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@ -94,6 +94,17 @@ enum _LMP_VAR_CONST {
LMP_VAR_STRING = 3 /*!< return value will be a string (catch-all) */
};
/** Neighbor list settings constants
*
* Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``,
* ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and
* ``examples/COUPLE/plugin/liblammpsplugin.h`` */
enum _LMP_NEIGH_CONST {
LMP_NEIGH_HALF = 0, /*!< request (default) half neighbor list */
LMP_NEIGH_FULL = 1, /*!< request full neighbor list */
};
#ifdef __cplusplus
extern "C" {
#endif
@ -189,14 +200,17 @@ struct _liblammpsplugin {
* caller must match to how LAMMPS library is built */
#if !defined(LAMMPS_BIGBIG)
int (*create_atoms)(void *, int, int *, int *, double *, double *, int *, int);
int (*create_atoms)(void *, int, const int *, const int *, const double *, const double *,
const int *, int);
#else
int (*create_atoms)(void *, int, int64_t *, int *, double *, double *, int64_t *, int);
int (*create_atoms)(void *, int, const int64_t *, const int *, const double *, const double *,
const int64_t *, int);
#endif
int (*find_pair_neighlist)(void *, const char *, int, int, int);
int (*find_fix_neighlist)(void *, const char *, int);
int (*find_compute_neighlist)(void *, const char *, int);
int (*request_single_neighlist)(void *, const char *, int, double);
int (*neighlist_num_elements)(void *, int);
void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);

2
examples/COUPLE/simple/CMakeLists.txt
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@ -25,10 +25,10 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
find_package(MPI QUIET)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET COMPONENTS C CXX)
##########################

6
examples/PACKAGES/apip/in.vacancy.const.lambda
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@ -20,9 +20,9 @@ read_data data.vacancy
group vacancy id 145 147 148 149 150 994 997 995 1024 1026 1028 1922
group transition id 77 79 81 84 88 151 152 153 154 155 158 1089 188 189 192 1033 1039 1964 1022 1021 999 998 996 948 950 952 992 993 139 1025 1027 1029 1034 1035 1038 1088 1920 1921 1923 1924 1925 1930
group bulk subtract all vacancy transition
set group vacancy apip_lambda precise
set group transition apip_lambda 0.5
set group bulk apip_lambda fast
set group vacancy apip/lambda precise
set group transition apip/lambda 0.5
set group bulk apip/lambda fast
fix nve all nve

4
examples/PACKAGES/apip/in.validate
View File

@ -38,11 +38,11 @@ pair_coeff * * eam/fs/apip ${eamfs_file} Cu
pair_coeff * * pace/apip ${ace_file} Cu
# use ACE of adaptive-precision potential
set group all apip_lambda precise
set group all apip/lambda precise
run 0
# use EAM of adaptive-precision potential
set group all apip_lambda fast
set group all apip/lambda fast
run 0
# Use EAM potential

4
examples/PACKAGES/imd/in.bucky-plus-cnt
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@ -46,8 +46,8 @@ fix integrate mobile nve
fix thermostat mobile langevin 300.0 300.0 2000.0 234624
# IMD setup.
fix comm all imd 6789 unwrap on trate 10
#fix comm all imd 6789 unwrap on trate 10 nowait on
#fix comm all imd 6789 unwrap on trate 10
fix comm all imd 6789 unwrap on trate 10 nowait on
# temperature is based on mobile atoms only
compute mobtemp mobile temp

15
examples/PACKAGES/imd/in.bucky-plus-cnt-gpu
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@ -1,16 +1,20 @@
# stick a buckyball into a nanotube
# enable GPU package from within the input:
package gpu 0 pair/only on
suffix gpu
units real
dimension 3
boundary f f f
atom_style molecular
newton off
processors * * 1
# read topology
read_data data.bucky-plus-cnt
pair_style lj/cut/gpu 10.0
pair_style lj/cut 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
@ -29,9 +33,6 @@ neigh_modify delay 0 every 1 check yes
timestep 2.0
# required for GPU acceleration
fix gpu all gpu force 0 0 1.0
# we only move some atoms.
group mobile type 1
@ -49,8 +50,8 @@ fix integrate mobile nve
fix thermostat mobile langevin 300.0 300.0 2000.0 234624
# IMD setup.
fix comm all imd 6789 unwrap on trate 10
#fix comm all imd 6789 unwrap on trate 10 nowait on
#fix comm all imd 6789 unwrap on trate 10
fix comm all imd 6789 unwrap on trate 10 nowait on
# temperature is based on mobile atoms only
compute mobtemp mobile temp

14
examples/PACKAGES/imd/in.deca-ala_imd-gpu
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@ -1,8 +1,12 @@
#
#
# enable GPU package from within the input:
package gpu 0 pair/only on
suffix gpu
units real
neighbor 2.5 bin
neigh_modify delay 1 every 1
newton off
atom_style full
bond_style harmonic
@ -10,20 +14,18 @@ angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8 10
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
special_bonds charmm
read_data data.deca-ala-solv
fix 0 all gpu force/neigh 0 0 1.0
group peptide id <= 103
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
thermo 100
thermo_style multi
timestep 2.0
kspace_style pppm/gpu 1e-5
kspace_style pppm 1e-5
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2

38
examples/PACKAGES/imd/in.melt_imd-gpu
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@ -1,30 +1,32 @@
# 3d Lennard-Jones melt
# 3d Lennard-Jones melt with GPU package acceleration
units lj
atom_style atomic
newton off
# enable GPU package from within the input:
package gpu 0
suffix gpu
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
units lj
atom_style atomic
velocity all create 3.0 87287
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut/gpu 2.5
pair_coeff 1 1 1.0 1.0 2.5
velocity all create 3.0 87287
neighbor 0.3 bin
neigh_modify every 5 delay 10 check yes
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 5 delay 10 check yes
thermo_style custom step pe ke spcpu
fix 0 all gpu force/neigh 0 0 1.0
fix 1 all nve
fix 1 all nve
# IMD setup.
fix comm all imd 5678 unwrap off fscale 20.0 trate 20 nowait on
thermo 500
run 5000000
thermo 500
run 5000000

35
examples/PACKAGES/moments/in.converge Normal file
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@ -0,0 +1,35 @@
# Detect convergence in a simulation using the relative change in
# moments. This demonstrates the "history" option.
# ---------------------------------------------------------------------
# create pure copper system
units metal
lattice fcc 3.75
region box block 0 6 0 6 0 6
create_box 2 box
timestep 0.002
create_atoms 1 box
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# Initialize to a high temperature, then cool in npt ensemble
velocity all create 1000.0 6567345
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
# compute mean and stddev over the preceding 5000 steps, every 20 steps
variable toteng equal "etotal"
fix 2 all ave/moments 10 500 200 v_toteng mean stddev history 5
# Convergence criterion: stddev is smaller than threshold and was previously larger
# This avoids issues with system oscillations in the order of the averaging window
# that would otherwise lead to "nodes" in the stddev.
variable conv equal "(f_2[2] < 2.0) && (f_2[2][1] < f_2[2][5])"
fix 3 all halt 100 v_conv == 1
thermo_style custom step temp press etotal f_2[*][1] f_2[*][5] v_conv
thermo 100
run 10000

27
examples/PACKAGES/moments/in.simple Normal file
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@ -0,0 +1,27 @@
# Perform a simple simulation and output the moments of the total energy
# ---------------------------------------------------------------------
# create pure copper system
units metal
lattice fcc 3.75
region box block 0 6 0 6 0 6
create_box 2 box
timestep 0.002
create_atoms 1 box
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# Initialize to a high temperature, then cool in npt ensemble
velocity all create 1000.0 6567345
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
variable toteng equal "etotal"
fix 2 all ave/moments 5 200 100 v_toteng mean stddev variance skew kurtosis
thermo_style custom step temp press etotal f_2[*]
thermo 100
run 10000

28
examples/PACKAGES/moments/in.valtest Normal file
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@ -0,0 +1,28 @@
# Output raw and computed data. This can be used to perform the moment
# calculation in some external tool and validate our results
# ---------------------------------------------------------------------
# create pure copper system
units metal
lattice fcc 3.75
region box block 0 6 0 6 0 6
create_box 2 box
timestep 0.002
create_atoms 1 box
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# Initialize to a high temperature, then cool in npt ensemble
velocity all create 1000.0 6567345
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
variable toteng equal "etotal"
fix 2 all ave/moments 1 10 10 v_toteng mean variance skew kurtosis
thermo_style custom step etotal f_2[*]
thermo_modify format float %14.8f
thermo 1
run 100

171
examples/PACKAGES/moments/log.02May2025.converge.g++.1 Normal file
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@ -0,0 +1,171 @@
LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# create pure copper system
units metal
lattice fcc 3.75
Lattice spacing in x,y,z = 3.75 3.75 3.75
region box block 0 6 0 6 0 6
create_box 2 box
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
1 by 1 by 1 MPI processor grid
timestep 0.002
create_atoms 1 box
Created 864 atoms
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
create_atoms CPU = 0.001 seconds
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# Initialize to a high temperature, then cool in npt ensemble
velocity all create 1000.0 6567345
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
variable toteng equal "etotal"
fix 2 all ave/moments 10 500 200 v_toteng mean stddev history 5
variable conv equal "(f_2[2] < 2) && (f_2[2][1] < f_2[2][5])"
fix 3 all halt 1000 v_conv == 1
thermo_style custom step temp press etotal f_2[*][1] f_2[*][5] v_conv
thermo 100
run 10000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, 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) = 3.484 | 3.484 | 3.484 Mbytes
Step Temp Press TotEng f_2[1][1] f_2[2][1] f_2[1][5] f_2[2][5] v_conv
0 1000 -107410.22 -2884.9159 0 0 0 0 0
100 512.04214 -124.66263 -2928.6 0 0 0 0 0
200 479.34328 -136.26635 -2931.3905 -2928.6251 2.1584834 0 0 0
300 480.05298 128.92946 -2933.9233 -2928.6251 2.1584834 0 0 0
400 471.83641 -29.253334 -2936.8631 -2931.3742 3.3668783 0 0 0
500 456.96309 -274.69336 -2939.9081 -2931.3742 3.3668783 0 0 0
600 450.32413 14.606227 -2942.973 -2934.277 5.0681849 0 0 0
700 431.71192 -45.641261 -2946.006 -2934.277 5.0681849 0 0 0
800 436.4217 589.91981 -2948.8885 -2937.2386 6.823233 0 0 0
900 407.84688 -3728.1499 -2951.6643 -2937.2386 6.823233 0 0 0
1000 401.69178 6695.3653 -2954.2959 -2940.1463 8.4728269 -2928.6251 2.1584834 0
1100 370.87469 -2294.843 -2956.9413 -2940.1463 8.4728269 -2928.6251 2.1584834 0
1200 375.15562 704.6568 -2959.3841 -2942.9613 10.001542 -2931.3742 3.3668783 0
1300 371.09077 -493.04016 -2961.6803 -2942.9613 10.001542 -2931.3742 3.3668783 0
1400 365.88512 490.98174 -2963.8365 -2945.6475 11.378724 -2934.277 5.0681849 0
1500 358.42655 -218.94911 -2965.8652 -2945.6475 11.378724 -2934.277 5.0681849 0
1600 329.08402 56.411923 -2967.7662 -2948.1844 12.597017 -2937.2386 6.823233 0
1700 317.74207 1192.918 -2969.557 -2948.1844 12.597017 -2937.2386 6.823233 0
1800 331.98966 -2205.7213 -2971.1465 -2950.559 13.653575 -2940.1463 8.4728269 0
1900 330.96814 1401.3066 -2972.6923 -2950.559 13.653575 -2940.1463 8.4728269 0
2000 315.41816 -909.41909 -2974.0785 -2952.7764 14.568194 -2942.9613 10.001542 0
2100 320.4269 1226.2006 -2975.3676 -2952.7764 14.568194 -2942.9613 10.001542 0
2200 302.88235 -1238.8052 -2976.5099 -2954.8327 15.341787 -2945.6475 11.378724 0
2300 300.4349 2667.202 -2977.5329 -2954.8327 15.341787 -2945.6475 11.378724 0
2400 292.94691 -5532.1854 -2978.3724 -2956.7266 15.978754 -2948.1844 12.597017 0
2500 286.12064 4647.3841 -2979.2217 -2956.7266 15.978754 -2948.1844 12.597017 0
2600 290.74305 -1950.526 -2979.9142 -2958.4592 16.485773 -2950.559 13.653575 0
2700 281.51347 937.60472 -2980.4808 -2958.4592 16.485773 -2950.559 13.653575 0
2800 279.71836 -801.62498 -2980.8899 -2960.032 16.869365 -2952.7764 14.568194 0
2900 277.41241 609.21495 -2981.1721 -2960.032 16.869365 -2952.7764 14.568194 0
3000 281.31161 -760.27203 -2981.3003 -2961.4399 17.128547 -2954.8327 15.341787 0
3100 284.72904 315.53038 -2981.297 -2961.4399 17.128547 -2954.8327 15.341787 0
3200 278.39445 516.25074 -2981.1224 -2962.6768 17.263037 -2956.7266 15.978754 0
3300 294.46998 -655.06212 -2980.8266 -2962.6768 17.263037 -2956.7266 15.978754 0
3400 290.04647 788.30424 -2980.3963 -2963.7417 17.280979 -2958.4592 16.485773 0
3500 283.218 -844.33188 -2979.8504 -2963.7417 17.280979 -2958.4592 16.485773 0
3600 288.76031 1339.2734 -2979.2382 -2964.6345 17.192698 -2960.032 16.869365 0
3700 289.44519 -3015.7161 -2978.5394 -2964.6345 17.192698 -2960.032 16.869365 0
3800 309.04206 5579.3265 -2977.8282 -2965.3649 17.01845 -2961.4399 17.128547 0
3900 309.34588 -4255.5213 -2977.1281 -2965.3649 17.01845 -2961.4399 17.128547 0
4000 305.79444 2358.1383 -2976.5251 -2965.9537 16.784519 -2962.6768 17.263037 0
4100 309.12957 -1401.6484 -2975.9173 -2965.9537 16.784519 -2962.6768 17.263037 0
4200 309.41928 1180.4111 -2975.3857 -2966.4277 16.516135 -2963.7417 17.280979 0
4300 299.88949 -1549.6591 -2974.927 -2966.4277 16.516135 -2963.7417 17.280979 0
4400 319.09918 1937.7006 -2974.5598 -2966.8138 16.232551 -2964.6345 17.192698 0
4500 326.48719 -1489.2073 -2974.311 -2966.8138 16.232551 -2964.6345 17.192698 0
4600 310.93392 37.586899 -2974.1959 -2967.1394 15.948448 -2965.3649 17.01845 0
4700 314.28994 317.12347 -2974.1763 -2967.1394 15.948448 -2965.3649 17.01845 0
4800 309.88756 -698.72705 -2974.2892 -2967.4334 15.675606 -2965.9537 16.784519 0
4900 309.53444 962.42921 -2974.5261 -2967.4334 15.675606 -2965.9537 16.784519 0
5000 316.06666 -1869.3275 -2974.8492 -2967.7182 15.421633 -2966.4277 16.516135 0
5100 304.82485 4042.6797 -2975.2715 -2967.7182 15.421633 -2966.4277 16.516135 0
5200 307.75342 -5058.4814 -2975.7195 -2969.5853 13.236776 -2966.8138 16.232551 0
5300 298.83511 3096.4566 -2976.3329 -2969.5853 13.236776 -2966.8138 16.232551 0
5400 296.85413 -1929.1654 -2976.8797 -2971.2747 11.121537 -2967.1394 15.948448 0
5500 295.88343 1449.3005 -2977.4488 -2971.2747 11.121537 -2967.1394 15.948448 0
5600 305.59328 -1504.0321 -2977.9573 -2972.77 9.1579616 -2967.4334 15.675606 0
5700 293.40683 2579.0134 -2978.4364 -2972.77 9.1579616 -2967.4334 15.675606 0
5800 297.93644 -2742.705 -2978.8276 -2974.0625 7.4101102 -2967.7182 15.421633 0
5900 290.39408 1189.4042 -2979.2224 -2974.0625 7.4101102 -2967.7182 15.421633 0
6000 293.73148 -232.54292 -2979.503 -2975.1594 5.8959922 -2969.5853 13.236776 0
6100 292.04933 -168.30971 -2979.6898 -2975.1594 5.8959922 -2969.5853 13.236776 0
6200 299.23747 839.17828 -2979.7883 -2976.0647 4.6378408 -2971.2747 11.121537 0
6300 294.92201 -1597.9426 -2979.7975 -2976.0647 4.6378408 -2971.2747 11.121537 0
6400 291.7185 3411.2916 -2979.6978 -2976.7848 3.643826 -2972.77 9.1579616 0
6500 285.34227 -4280.7968 -2979.4874 -2976.7848 3.643826 -2972.77 9.1579616 0
6600 295.53838 2138.7496 -2979.2799 -2977.3265 2.9178925 -2974.0625 7.4101102 0
6700 288.54718 -1818.7662 -2978.9379 -2977.3265 2.9178925 -2974.0625 7.4101102 0
6800 290.41342 2175.3559 -2978.543 -2977.7009 2.4532223 -2975.1594 5.8959922 0
6900 296.34456 -4782.08 -2978.0362 -2977.7009 2.4532223 -2975.1594 5.8959922 0
7000 303.74314 5905.219 -2977.577 -2977.9137 2.2279716 -2976.0647 4.6378408 0
7100 303.90284 -3291.7627 -2977.1308 -2977.9137 2.2279716 -2976.0647 4.6378408 0
7200 296.13966 2209.574 -2976.7001 -2977.9829 2.1708943 -2976.7848 3.643826 0
7300 295.79694 -1609.1898 -2976.2816 -2977.9829 2.1708943 -2976.7848 3.643826 0
7400 306.53289 988.50902 -2975.8992 -2977.931 2.1935882 -2977.3265 2.9178925 0
7500 303.89992 -631.22838 -2975.5597 -2977.931 2.1935882 -2977.3265 2.9178925 0
7600 303.83684 -348.48744 -2975.3074 -2977.7831 2.2226664 -2977.7009 2.4532223 0
7700 309.67313 1350.9414 -2975.1279 -2977.7831 2.2226664 -2977.7009 2.4532223 0
7800 309.74314 -1182.8905 -2975.0174 -2977.5683 2.2106484 -2977.9137 2.2279716 0
7900 309.42429 999.08033 -2975.0089 -2977.5683 2.2106484 -2977.9137 2.2279716 0
8000 315.51872 -1337.8894 -2975.0791 -2977.3233 2.1379295 -2977.9829 2.1708943 0
8100 314.80533 2392.3424 -2975.25 -2977.3233 2.1379295 -2977.9829 2.1708943 0
8200 303.80236 -3224.5976 -2975.4744 -2977.0851 2.0176342 -2977.931 2.1935882 0
8300 295.0505 3296.6912 -2975.8196 -2977.0851 2.0176342 -2977.931 2.1935882 0
8400 302.4154 -3314.5096 -2976.1586 -2976.8877 1.883051 -2977.7831 2.2226664 1
8500 300.95491 2971.1291 -2976.5859 -2976.8877 1.883051 -2977.7831 2.2226664 1
8600 301.68919 -2297.6673 -2976.9953 -2976.7596 1.785401 -2977.5683 2.2106484 1
8700 291.21002 1477.5703 -2977.4323 -2976.7596 1.785401 -2977.5683 2.2106484 1
8800 305.87126 -1085.459 -2977.8247 -2976.7169 1.7541517 -2977.3233 2.1379295 1
8900 296.17567 777.95805 -2978.2081 -2976.7169 1.7541517 -2977.3233 2.1379295 1
Fix halt condition for fix-id 3 met on step 9000 with value 1 (src/fix_halt.cpp:310)
9000 295.71917 -425.00708 -2978.5264 -2976.7595 1.7755885 -2977.0851 2.0176342 1
Loop time of 42.1758 on 1 procs for 9000 steps with 864 atoms
Performance: 36.874 ns/day, 0.651 hours/ns, 213.393 timesteps/s, 184.371 katom-step/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 | 41.126 | 41.126 | 41.126 | 0.0 | 97.51
Neigh | 0.0078787 | 0.0078787 | 0.0078787 | 0.0 | 0.02
Comm | 0.26508 | 0.26508 | 0.26508 | 0.0 | 0.63
Output | 0.0096224 | 0.0096224 | 0.0096224 | 0.0 | 0.02
Modify | 0.65597 | 0.65597 | 0.65597 | 0.0 | 1.56
Other | | 0.1108 | | | 0.26
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3767 ave 3767 max 3767 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 96746 ave 96746 max 96746 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 96746
Ave neighs/atom = 111.97454
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:42

171
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LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# create pure copper system
units metal
lattice fcc 3.75
Lattice spacing in x,y,z = 3.75 3.75 3.75
region box block 0 6 0 6 0 6
create_box 2 box
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
1 by 2 by 2 MPI processor grid
timestep 0.002
create_atoms 1 box
Created 864 atoms
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
create_atoms CPU = 0.001 seconds
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# Initialize to a high temperature, then cool in npt ensemble
velocity all create 1000.0 6567345
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
variable toteng equal "etotal"
fix 2 all ave/moments 10 500 200 v_toteng mean stddev history 5
variable conv equal "(f_2[2] < 2) && (f_2[2][1] < f_2[2][5])"
fix 3 all halt 1000 v_conv == 1
thermo_style custom step temp press etotal f_2[*][1] f_2[*][5] v_conv
thermo 100
run 10000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, 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) = 3.42 | 3.42 | 3.42 Mbytes
Step Temp Press TotEng f_2[1][1] f_2[2][1] f_2[1][5] f_2[2][5] v_conv
0 1000 -107410.22 -2884.9159 0 0 0 0 0
100 492.38014 -134.33622 -2928.6874 0 0 0 0 0
200 484.82396 -214.26318 -2931.4603 -2928.6979 2.1805063 0 0 0
300 476.69743 15.78678 -2934.0022 -2928.6979 2.1805063 0 0 0
400 482.51415 141.67184 -2936.9347 -2931.4437 3.3715811 0 0 0
500 455.45411 2.4424602 -2939.9649 -2931.4437 3.3715811 0 0 0
600 455.20054 -6.8170934 -2943.0454 -2934.339 5.0598781 0 0 0
700 429.81168 -75.812923 -2946.0438 -2934.339 5.0598781 0 0 0
800 428.22097 604.18705 -2948.9285 -2937.2965 6.813037 0 0 0
900 399.10914 -3622.6904 -2951.7252 -2937.2965 6.813037 0 0 0
1000 394.62543 7905.9041 -2954.2925 -2940.2044 8.4668749 -2928.6979 2.1805063 0
1100 404.27007 -2565.5508 -2956.9736 -2940.2044 8.4668749 -2928.6979 2.1805063 0
1200 368.47178 741.43707 -2959.4264 -2943.0151 9.9914785 -2931.4437 3.3715811 0
1300 360.91266 -267.08372 -2961.69 -2943.0151 9.9914785 -2931.4437 3.3715811 0
1400 356.74405 158.09093 -2963.8501 -2945.696 11.36357 -2934.339 5.0598781 0
1500 335.45696 -71.007783 -2965.8817 -2945.696 11.36357 -2934.339 5.0598781 0
1600 331.01199 -454.90004 -2967.7708 -2948.2278 12.577884 -2937.2965 6.813037 0
1700 329.223 2428.4284 -2969.5452 -2948.2278 12.577884 -2937.2965 6.813037 0
1800 327.61481 -4757.648 -2971.1105 -2950.5985 13.632251 -2940.2044 8.4668749 0
1900 318.18741 2226.7765 -2972.6906 -2950.5985 13.632251 -2940.2044 8.4668749 0
2000 308.79313 -1089.8603 -2974.0899 -2952.8123 14.545164 -2943.0151 9.9914785 0
2100 303.32047 757.53534 -2975.3597 -2952.8123 14.545164 -2943.0151 9.9914785 0
2200 307.41102 -837.97246 -2976.4966 -2954.8654 15.317558 -2945.696 11.36357 0
2300 303.01088 1618.29 -2977.5454 -2954.8654 15.317558 -2945.696 11.36357 0
2400 297.59385 -3233.8282 -2978.4064 -2956.7565 15.953758 -2948.2278 12.577884 0
2500 288.72232 5209.2099 -2979.1999 -2956.7565 15.953758 -2948.2278 12.577884 0
2600 298.92201 -2193.618 -2979.8873 -2958.4845 16.457635 -2950.5985 13.632251 0
2700 282.61818 765.88178 -2980.4563 -2958.4845 16.457635 -2950.5985 13.632251 0
2800 273.63104 -389.49749 -2980.8636 -2960.0533 16.839029 -2952.8123 14.545164 0
2900 274.12166 -9.2552992 -2981.1421 -2960.0533 16.839029 -2952.8123 14.545164 0
3000 279.43592 212.25445 -2981.2716 -2961.4578 17.096628 -2954.8654 15.317558 0
3100 291.10071 -1139.205 -2981.2475 -2961.4578 17.096628 -2954.8654 15.317558 0
3200 281.53171 3124.6411 -2981.0818 -2962.6921 17.230604 -2956.7565 15.953758 0
3300 277.0223 -2795.9494 -2980.7825 -2962.6921 17.230604 -2956.7565 15.953758 0
3400 284.8443 1587.8876 -2980.3701 -2963.754 17.247489 -2958.4845 16.457635 0
3500 281.19 -1143.0785 -2979.8374 -2963.754 17.247489 -2958.4845 16.457635 0
3600 296.58287 1156.4706 -2979.2182 -2964.645 17.159411 -2960.0533 16.839029 0
3700 297.24517 -1888.4993 -2978.5352 -2964.645 17.159411 -2960.0533 16.839029 0
3800 290.81586 3843.3483 -2977.8509 -2965.3746 16.985916 -2961.4578 17.096628 0
3900 300.39456 -5584.8386 -2977.0837 -2965.3746 16.985916 -2961.4578 17.096628 0
4000 306.15811 3310.0105 -2976.5086 -2965.9619 16.752214 -2962.6921 17.230604 0
4100 295.907 -1475.0458 -2975.9096 -2965.9619 16.752214 -2962.6921 17.230604 0
4200 322.70162 933.76586 -2975.3867 -2966.4348 16.484219 -2963.754 17.247489 0
4300 306.69631 -512.7048 -2974.9324 -2966.4348 16.484219 -2963.754 17.247489 0
4400 309.23776 226.77219 -2974.5791 -2966.8208 16.201471 -2964.645 17.159411 0
4500 313.15783 508.29785 -2974.3263 -2966.8208 16.201471 -2964.645 17.159411 0
4600 316.26151 -2043.7571 -2974.1697 -2967.1463 15.918137 -2965.3746 16.985916 0
4700 312.27329 1831.682 -2974.1732 -2967.1463 15.918137 -2965.3746 16.985916 0
4800 307.61066 -1476.0019 -2974.2885 -2967.4397 15.645834 -2965.9619 16.752214 0
4900 305.73489 1303.4848 -2974.5506 -2967.4397 15.645834 -2965.9619 16.752214 0
5000 309.3774 -1574.6812 -2974.8687 -2967.7249 15.392787 -2966.4348 16.484219 0
5100 304.8602 2679.7476 -2975.3082 -2967.7249 15.392787 -2966.4348 16.484219 0
5200 297.54226 -5008.0905 -2975.7443 -2969.5904 13.211657 -2966.8208 16.201471 0
5300 306.18872 4840.4175 -2976.324 -2969.5904 13.211657 -2966.8208 16.201471 0
5400 299.57661 -2513.1706 -2976.8842 -2971.2774 11.099846 -2967.1463 15.918137 0
5500 302.30844 1301.3525 -2977.4539 -2971.2774 11.099846 -2967.1463 15.918137 0
5600 302.11038 -760.79712 -2977.9764 -2972.7712 9.1381778 -2967.4397 15.645834 0
5700 294.49825 718.67318 -2978.4584 -2972.7712 9.1381778 -2967.4397 15.645834 0
5800 305.97636 -478.64224 -2978.8638 -2974.0628 7.3929182 -2967.7249 15.392787 0
5900 291.93868 -419.74179 -2979.2292 -2974.0628 7.3929182 -2967.7249 15.392787 0
6000 289.50667 859.85085 -2979.5018 -2975.1575 5.8837236 -2969.5904 13.211657 0
6100 305.70118 -933.35917 -2979.6877 -2975.1575 5.8837236 -2969.5904 13.211657 0
6200 284.37805 1526.0707 -2979.806 -2976.062 4.6281363 -2971.2774 11.099846 0
6300 291.08863 -2156.6708 -2979.8064 -2976.062 4.6281363 -2971.2774 11.099846 0
6400 295.99073 2819.8245 -2979.7378 -2976.7827 3.6358684 -2972.7712 9.1381778 0
6500 298.06769 -3396.3504 -2979.5428 -2976.7827 3.6358684 -2972.7712 9.1381778 0
6600 301.78514 5496.6525 -2979.2768 -2977.3261 2.9112079 -2974.0628 7.3929182 0
6700 290.80665 -5229.4989 -2978.9177 -2977.3261 2.9112079 -2974.0628 7.3929182 0
6800 296.75761 2401.7807 -2978.5996 -2977.7014 2.4473856 -2975.1575 5.8837236 0
6900 295.77553 -1521.6269 -2978.1619 -2977.7014 2.4473856 -2975.1575 5.8837236 0
7000 303.59015 1530.7255 -2977.7097 -2977.9176 2.2219164 -2976.062 4.6281363 0
7100 297.51038 -3016.4426 -2977.2025 -2977.9176 2.2219164 -2976.062 4.6281363 0
7200 293.53789 2705.9808 -2976.7651 -2977.9894 2.1638143 -2976.7827 3.6358684 0
7300 301.78809 -1042.1076 -2976.3388 -2977.9894 2.1638143 -2976.7827 3.6358684 0
7400 307.50053 214.56923 -2975.9581 -2977.9394 2.1852009 -2977.3261 2.9112079 0
7500 301.98985 281.86495 -2975.6146 -2977.9394 2.1852009 -2977.3261 2.9112079 0
7600 318.37347 -1145.7795 -2975.3473 -2977.7949 2.2136707 -2977.7014 2.4473856 0
7700 314.94512 4536.9887 -2975.1351 -2977.7949 2.2136707 -2977.7014 2.4473856 0
7800 312.91485 -2980.6408 -2975.0156 -2977.5818 2.2038198 -2977.9176 2.2219164 0
7900 310.06854 2244.3877 -2975.0094 -2977.5818 2.2038198 -2977.9176 2.2219164 0
8000 308.55007 -2427.1464 -2975.0491 -2977.3378 2.1348358 -2977.9894 2.1638143 0
8100 323.02796 3187.4728 -2975.2081 -2977.3378 2.1348358 -2977.9894 2.1638143 0
8200 327.05029 -6447.7875 -2975.3162 -2977.0986 2.0196599 -2977.9394 2.1852009 0
8300 311.194 4273.1174 -2975.7217 -2977.0986 2.0196599 -2977.9394 2.1852009 0
8400 290.61931 -2301.019 -2976.0963 -2976.8989 1.8918948 -2977.7949 2.2136707 1
8500 314.00559 1966.1297 -2976.5206 -2976.8989 1.8918948 -2977.7949 2.2136707 1
8600 288.26541 -1608.4524 -2976.9304 -2976.7685 1.7971228 -2977.5818 2.2038198 1
8700 298.92083 1353.9988 -2977.355 -2976.7685 1.7971228 -2977.5818 2.2038198 1
8800 299.97274 -638.68301 -2977.766 -2976.722 1.7650747 -2977.3378 2.1348358 1
8900 300.66443 -279.62514 -2978.1476 -2976.722 1.7650747 -2977.3378 2.1348358 1
Fix halt condition for fix-id 3 met on step 9000 with value 1 (src/fix_halt.cpp:310)
9000 290.44715 489.06352 -2978.4892 -2976.7631 1.7846181 -2977.0986 2.0196599 1
Loop time of 14.7347 on 4 procs for 9000 steps with 864 atoms
Performance: 105.547 ns/day, 0.227 hours/ns, 610.804 timesteps/s, 527.735 katom-step/s
92.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.565 | 11.474 | 12.015 | 16.1 | 77.87
Neigh | 0.0020313 | 0.0020966 | 0.002163 | 0.1 | 0.01
Comm | 2.008 | 2.5374 | 3.4278 | 33.5 | 17.22
Output | 0.0030284 | 0.0036299 | 0.0051776 | 1.5 | 0.02
Modify | 0.42442 | 0.43307 | 0.44329 | 1.0 | 2.94
Other | | 0.2849 | | | 1.93
Nlocal: 216 ave 224 max 204 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Nghost: 2147 ave 2159 max 2139 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 24185.8 ave 26045 max 21309 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 96743
Ave neighs/atom = 111.97106
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:14

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LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# create pure copper system
units metal
lattice fcc 3.75
Lattice spacing in x,y,z = 3.75 3.75 3.75
region box block 0 6 0 6 0 6
create_box 2 box
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
1 by 1 by 1 MPI processor grid
timestep 0.002
create_atoms 1 box
Created 864 atoms
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
create_atoms CPU = 0.001 seconds
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# Initialize to a high temperature, then cool in npt ensemble
velocity all create 1000.0 6567345
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
variable toteng equal "etotal"
fix 2 all ave/moments 5 200 100 v_toteng mean stddev variance skew kurtosis
thermo_style custom step temp press etotal f_2[*]
thermo 100
run 10000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, 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) = 3.484 | 3.484 | 3.484 Mbytes
Step Temp Press TotEng f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]
0 1000 -107410.22 -2884.9159 0 0 0 0 0
100 512.04214 -124.66263 -2928.6 -2927.1688 1.6797138 2.8214386 2.5218138 6.164012
200 479.34328 -136.26635 -2931.3905 -2928.6374 1.9791406 3.9169976 1.3377745 3.2426285
300 480.05298 128.92946 -2933.9233 -2929.9825 2.5401119 6.4521682 0.66415393 0.77130236
400 471.83641 -29.253334 -2936.8631 -2931.346 3.2640831 10.654239 0.29075579 -0.26904542
500 456.96309 -274.69336 -2939.9081 -2932.7721 4.1077082 16.873267 0.094954709 -0.72240572
600 450.32413 14.606227 -2942.973 -2934.2328 4.9928765 24.928816 0.0090731063 -0.93757177
700 431.71192 -45.641261 -2946.006 -2935.7111 5.8871117 34.658084 -0.024573652 -1.0540107
800 436.4217 589.91981 -2948.8885 -2937.1871 6.762411 45.730202 -0.028553126 -1.1275153
900 407.84688 -3728.1499 -2951.6643 -2938.652 7.6129868 57.957569 -0.020186137 -1.172618
1000 401.69178 6695.3653 -2954.2959 -2940.0921 8.423174 70.949861 -0.0018224075 -1.2051609
1100 370.87469 -2294.843 -2956.9413 -2942.9469 8.384346 70.297257 0.016964628 -1.2643199
1200 375.15562 704.6568 -2959.3841 -2945.7589 8.3201293 69.224551 0.070500644 -1.2400262
1300 371.09077 -493.04016 -2961.6803 -2948.5516 8.1425118 66.300499 0.11183042 -1.2099873
1400 365.88512 490.98174 -2963.8365 -2951.2897 7.8673969 61.895934 0.13639588 -1.198071
1500 358.42655 -218.94911 -2965.8652 -2953.9337 7.5491659 56.989906 0.15564307 -1.1896984
1600 329.08402 56.411923 -2967.7662 -2956.467 7.2016413 51.863637 0.17198437 -1.186472
1700 317.74207 1192.918 -2969.557 -2958.8765 6.8379658 46.757776 0.19041811 -1.1812241
1800 331.98966 -2205.7213 -2971.1465 -2961.1601 6.4614065 41.749774 0.20925197 -1.1714131
1900 330.96814 1401.3066 -2972.6923 -2963.3191 6.0867317 37.048302 0.22552163 -1.1523125
2000 315.41816 -909.41909 -2974.0785 -2965.3567 5.7020261 32.513101 0.2328316 -1.1454375
2100 320.4269 1226.2006 -2975.3676 -2967.2609 5.3260556 28.366869 0.24130517 -1.1432352
2200 302.88235 -1238.8052 -2976.5099 -2969.0355 4.9584282 24.58601 0.25200271 -1.141699
2300 300.4349 2667.202 -2977.5329 -2970.6815 4.5986371 21.147463 0.26764984 -1.1380521
2400 292.94691 -5532.1854 -2978.3724 -2972.201 4.2403749 17.980779 0.28797864 -1.1357902
2500 286.12064 4647.3841 -2979.2217 -2973.5946 3.8875889 15.113348 0.31556585 -1.1249025
2600 290.74305 -1950.526 -2979.9142 -2974.8686 3.5422986 12.547879 0.34719546 -1.0987558
2700 281.51347 937.60472 -2980.4808 -2976.0235 3.1955646 10.211633 0.38268676 -1.0664838
2800 279.71836 -801.62498 -2980.8899 -2977.0588 2.844105 8.0889331 0.41930147 -1.0460672
2900 277.41241 609.21495 -2981.1721 -2977.9673 2.4956133 6.2280855 0.47337432 -1.0140054
3000 281.31161 -760.27203 -2981.3003 -2978.7489 2.1466012 4.6078967 0.55325134 -0.95161956
3100 284.72904 315.53038 -2981.297 -2979.4023 1.7929581 3.2146986 0.66481771 -0.84726207
3200 278.39445 516.25074 -2981.1224 -2979.9226 1.4369984 2.0649644 0.82583409 -0.63830994
3300 294.46998 -655.06212 -2980.8266 -2980.3134 1.0905211 1.1892364 1.0357766 -0.22841943
3400 290.04647 788.30424 -2980.3963 -2980.5732 0.77030961 0.59337689 1.1867647 0.34447355
3500 283.218 -844.33188 -2979.8504 -2980.6995 0.54590076 0.29800764 0.78163948 -0.42619888
3600 288.76031 1339.2734 -2979.2382 -2980.6921 0.56032295 0.31396181 0.83603869 -0.30853278
3700 289.44519 -3015.7161 -2978.5394 -2980.5581 0.77708069 0.60385439 1.0796997 -0.022962365
3800 309.04206 5579.3265 -2977.8282 -2980.3052 1.0531468 1.1091181 0.890018 -0.56034495
3900 309.34588 -4255.5213 -2977.1281 -2979.9487 1.3153981 1.7302721 0.65242676 -0.95498589
4000 305.79444 2358.1383 -2976.5251 -2979.5068 1.5325477 2.3487025 0.44420123 -1.1839975
4100 309.12957 -1401.6484 -2975.9173 -2978.9985 1.6923829 2.86416 0.26850538 -1.3006942
4200 309.41928 1180.4111 -2975.3857 -2978.4446 1.7941259 3.2188877 0.11443933 -1.3365167
4300 299.88949 -1549.6591 -2974.927 -2977.8616 1.8268192 3.3372683 -0.018659059 -1.3293426
4400 319.09918 1937.7006 -2974.5598 -2977.273 1.7942266 3.219249 -0.13743367 -1.2958767
4500 326.48719 -1489.2073 -2974.311 -2976.7017 1.7042328 2.9044096 -0.25309558 -1.2385503
4600 310.93392 37.586899 -2974.1959 -2976.1697 1.5590672 2.4306905 -0.3757949 -1.1641151
4700 314.28994 317.12347 -2974.1763 -2975.6978 1.3661244 1.8662958 -0.51792367 -1.0609001
4800 309.88756 -698.72705 -2974.2892 -2975.3021 1.1422822 1.3048085 -0.69587053 -0.87319738
4900 309.53444 962.42921 -2974.5261 -2974.9944 0.89961859 0.80931361 -0.91892105 -0.49661907
5000 316.06666 -1869.3275 -2974.8492 -2974.7804 0.65817496 0.43319428 -1.0974595 0.048447651
5100 304.82485 4042.6797 -2975.2715 -2974.6661 0.47073268 0.22158926 -0.82059377 -0.31531887
5200 307.75342 -5058.4814 -2975.7195 -2974.6547 0.44733518 0.20010876 -0.68956594 -0.65171579
5300 298.83511 3096.4566 -2976.3329 -2974.7467 0.60599527 0.36723026 -1.0652601 0.032591262
5400 296.85413 -1929.1654 -2976.8797 -2974.9367 0.82832935 0.68612952 -0.91576774 -0.50322222
5500 295.88343 1449.3005 -2977.4488 -2975.215 1.044317 1.090598 -0.67574925 -0.92510515
5600 305.59328 -1504.0321 -2977.9573 -2975.5653 1.2243609 1.4990595 -0.46160433 -1.1708115
5700 293.40683 2579.0134 -2978.4364 -2975.97 1.3577316 1.843435 -0.27746111 -1.2993802
5800 297.93644 -2742.705 -2978.8276 -2976.411 1.4332742 2.054275 -0.11245859 -1.3584974
5900 290.39408 1189.4042 -2979.2224 -2976.8733 1.4576633 2.1247823 0.030209056 -1.3466833
6000 293.73148 -232.54292 -2979.503 -2977.3408 1.4300816 2.0451335 0.15663025 -1.2965878
6100 292.04933 -168.30971 -2979.6898 -2977.7936 1.3523929 1.8289665 0.28027258 -1.2214523
6200 299.23747 839.17828 -2979.7883 -2978.2154 1.2284868 1.5091798 0.40149929 -1.1382373
6300 294.92201 -1597.9426 -2979.7975 -2978.589 1.072002 1.1491883 0.53769821 -1.0262094
6400 291.7185 3411.2916 -2979.6978 -2978.9013 0.89165749 0.79505308 0.70748196 -0.83601078
6500 285.34227 -4280.7968 -2979.4874 -2979.1407 0.69727552 0.48619315 0.91500724 -0.4890805
6600 295.53838 2138.7496 -2979.2799 -2979.3084 0.50938648 0.25947459 1.0827149 -0.0043801382
6700 288.54718 -1818.7662 -2978.9379 -2979.3979 0.3658125 0.13381879 0.85573626 -0.20104653
6800 290.41342 2175.3559 -2978.543 -2979.4085 0.34439248 0.11860618 0.70989241 -0.55138716
6900 296.34456 -4782.08 -2978.0362 -2979.3362 0.47081063 0.22166265 1.1051059 0.16381282
7000 303.74314 5905.219 -2977.577 -2979.182 0.65635739 0.43080502 0.97456755 -0.34269231
7100 303.90284 -3291.7627 -2977.1308 -2978.9595 0.83412944 0.69577192 0.71973637 -0.85687335
7200 296.13966 2209.574 -2976.7001 -2978.6767 0.98885368 0.97783159 0.50554418 -1.124705
7300 295.79694 -1609.1898 -2976.2816 -2978.3446 1.1093729 1.2307082 0.32952142 -1.2657581
7400 306.53289 988.50902 -2975.8992 -2977.977 1.1910167 1.4185209 0.17936365 -1.331845
7500 303.89992 -631.22838 -2975.5597 -2977.5901 1.2352698 1.5258915 0.033110856 -1.3362459
7600 303.83684 -348.48744 -2975.3074 -2977.1915 1.2312686 1.5160224 -0.094817417 -1.3063491
7700 309.67313 1350.9414 -2975.1279 -2976.7984 1.1829266 1.3993154 -0.21343083 -1.2573517
7800 309.74314 -1182.8905 -2975.0174 -2976.4294 1.0913021 1.1909402 -0.3401118 -1.198459
7900 309.42429 999.08033 -2975.0089 -2976.0995 0.96393318 0.92916717 -0.48456322 -1.1149956
8000 315.51872 -1337.8894 -2975.0791 -2975.822 0.81535467 0.66480324 -0.67906685 -0.90499956
8100 314.80533 2392.3424 -2975.25 -2975.6019 0.64582022 0.41708376 -0.90521871 -0.5328796
8200 303.80236 -3224.5976 -2975.4744 -2975.4481 0.47449379 0.22514436 -1.0884377 -0.00018150871
8300 295.0505 3296.6912 -2975.8196 -2975.3667 0.34164698 0.11672266 -0.83269043 -0.31809119
8400 302.4154 -3314.5096 -2976.1586 -2975.3606 0.32904826 0.10827276 -0.73500255 -0.57861735
8500 300.95491 2971.1291 -2976.5859 -2975.4288 0.44584452 0.19877734 -1.0760301 0.014924509
8600 301.68919 -2297.6673 -2976.9953 -2975.5682 0.60852433 0.37030186 -0.91802963 -0.5143582
8700 291.21002 1477.5703 -2977.4323 -2975.7733 0.76843347 0.59048999 -0.68059043 -0.92051715
8800 305.87126 -1085.459 -2977.8247 -2976.0327 0.90672273 0.82214612 -0.47413162 -1.1492716
8900 296.17567 777.95805 -2978.2081 -2976.3349 1.0129061 1.0259789 -0.29734681 -1.271416
9000 295.71917 -425.00708 -2978.5264 -2976.6672 1.0786137 1.1634075 -0.14055755 -1.3302079
9100 296.85578 -533.46289 -2978.8197 -2977.0152 1.1000855 1.2101882 0.0045950751 -1.3434868
9200 293.949 605.27065 -2979.0349 -2977.3702 1.0854405 1.1781811 0.123965 -1.3093197
9300 289.11704 -896.44753 -2979.1981 -2977.7166 1.0353526 1.071955 0.23898813 -1.2558296
9400 285.34521 1181.7542 -2979.2879 -2978.0404 0.95298596 0.90818224 0.36461645 -1.1736585
9500 296.17714 -2503.9848 -2979.2668 -2978.3301 0.8407037 0.70678272 0.50841734 -1.0540275
9600 296.43744 4912.6395 -2979.1829 -2978.5736 0.70352404 0.49494608 0.68312042 -0.86335848
9700 288.63317 -3935.8902 -2979.0381 -2978.7635 0.55322477 0.30605764 0.88509388 -0.54108379
9800 296.27133 1365.4106 -2978.8723 -2978.8969 0.40665162 0.16536554 1.0460992 -0.092552905
9900 299.37628 -1267.2668 -2978.5934 -2978.9673 0.29467695 0.086834506 0.80391757 -0.38307943
10000 296.60645 1950.1018 -2978.2725 -2978.9739 0.28169006 0.079349287 0.70171659 -0.62026504
Loop time of 47.4814 on 1 procs for 10000 steps with 864 atoms
Performance: 36.393 ns/day, 0.659 hours/ns, 210.609 timesteps/s, 181.966 katom-step/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 | 46.299 | 46.299 | 46.299 | 0.0 | 97.51
Neigh | 0.010908 | 0.010908 | 0.010908 | 0.0 | 0.02
Comm | 0.29643 | 0.29643 | 0.29643 | 0.0 | 0.62
Output | 0.0090682 | 0.0090682 | 0.0090682 | 0.0 | 0.02
Modify | 0.7406 | 0.7406 | 0.7406 | 0.0 | 1.56
Other | | 0.1254 | | | 0.26
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3767 ave 3767 max 3767 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 96746 ave 96746 max 96746 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 96746
Ave neighs/atom = 111.97454
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:47

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LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# create pure copper system
units metal
lattice fcc 3.75
Lattice spacing in x,y,z = 3.75 3.75 3.75
region box block 0 6 0 6 0 6
create_box 2 box
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
1 by 2 by 2 MPI processor grid
timestep 0.002
create_atoms 1 box
Created 864 atoms
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
create_atoms CPU = 0.010 seconds
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# Initialize to a high temperature, then cool in npt ensemble
velocity all create 1000.0 6567345
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
variable toteng equal "etotal"
fix 2 all ave/moments 5 200 100 v_toteng mean stddev variance skew kurtosis
thermo_style custom step temp press etotal f_2[*]
thermo 100
run 10000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, 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) = 3.42 | 3.42 | 3.42 Mbytes
Step Temp Press TotEng f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]
0 1000 -107410.22 -2884.9159 0 0 0 0 0
100 492.38014 -134.33622 -2928.6874 -2927.2291 1.7092959 2.9216925 2.5081594 6.099781
200 484.82396 -214.26318 -2931.4603 -2928.71 2.0003214 4.0012857 1.3645049 3.3103886
300 476.69743 15.78678 -2934.0022 -2930.0515 2.5470901 6.4876682 0.6954232 0.86102766
400 482.51415 141.67184 -2936.9347 -2931.4152 3.2681043 10.680505 0.30641098 -0.22337036
500 455.45411 2.4424602 -2939.9649 -2932.8397 4.1076295 16.87262 0.10483325 -0.6997127
600 455.20054 -6.8170934 -2943.0454 -2934.2947 4.9842257 24.842506 0.018003661 -0.92490336
700 429.81168 -75.812923 -2946.0438 -2935.7704 5.8766819 34.53539 -0.019539731 -1.0444564
800 428.22097 604.18705 -2948.9285 -2937.2449 6.7522047 45.592268 -0.026384526 -1.1194924
900 399.10914 -3622.6904 -2951.7252 -2938.7094 7.6043904 57.826753 -0.019997758 -1.1658244
1000 394.62543 7905.9041 -2954.2925 -2940.15 8.4168551 70.84345 -0.0026187371 -1.2004009
1100 404.27007 -2565.5508 -2956.9736 -2943.0009 8.3722389 70.094384 0.015852037 -1.2665587
1200 368.47178 741.43707 -2959.4264 -2945.8091 8.3127243 69.101386 0.069744698 -1.2412651
1300 360.91266 -267.08372 -2961.69 -2948.5981 8.1334656 66.153263 0.1116445 -1.2129213
1400 356.74405 158.09093 -2963.8501 -2951.3302 7.8574973 61.740264 0.13825232 -1.1999727
1500 335.45696 -71.007783 -2965.8817 -2953.9689 7.5384846 56.82875 0.15915227 -1.1877331
1600 331.01199 -454.90004 -2967.7708 -2956.5 7.1862592 51.642321 0.17403957 -1.1840985
1700 329.223 2428.4284 -2969.5452 -2958.9073 6.8228029 46.55064 0.19027454 -1.1778276
1800 327.61481 -4757.648 -2971.1105 -2961.1863 6.4445074 41.531675 0.20819854 -1.1712539
1900 318.18741 2226.7765 -2972.6906 -2963.3396 6.0703365 36.848986 0.22378928 -1.1556732
2000 308.79313 -1089.8603 -2974.0899 -2965.3712 5.6913723 32.391718 0.23279863 -1.1445916
2100 303.32047 757.53534 -2975.3597 -2967.2741 5.3153102 28.252523 0.23857925 -1.1465858
2200 307.41102 -837.97246 -2976.4966 -2969.0433 4.9515105 24.517456 0.25216298 -1.1426077
2300 303.01088 1618.29 -2977.5454 -2970.6862 4.593227 21.097734 0.26914071 -1.1356519
2400 297.59385 -3233.8282 -2978.4064 -2972.2049 4.235209 17.936995 0.28804295 -1.1332908
2500 288.72232 5209.2099 -2979.1999 -2973.5963 3.8804647 15.058006 0.31533205 -1.1258312
2600 298.92201 -2193.618 -2979.8873 -2974.8649 3.5301507 12.461964 0.34927897 -1.1048024
2700 282.61818 765.88178 -2980.4563 -2976.0148 3.1852407 10.145758 0.3879755 -1.0655899
2800 273.63104 -389.49749 -2980.8636 -2977.0468 2.8322558 8.021673 0.4259426 -1.0370247
2900 274.12166 -9.2552992 -2981.1421 -2977.9525 2.4816703 6.1586877 0.47721359 -1.0061337
3000 279.43592 212.25445 -2981.2716 -2978.7309 2.1328425 4.5490171 0.5532015 -0.94983292
3100 291.10071 -1139.205 -2981.2475 -2979.3812 1.7828537 3.1785674 0.66452451 -0.83906914
3200 281.53171 3124.6411 -2981.0818 -2979.9003 1.4287164 2.0412304 0.81952022 -0.6386061
3300 277.0223 -2795.9494 -2980.7825 -2980.287 1.0830229 1.1729385 1.0186688 -0.26502454
3400 284.8443 1587.8876 -2980.3701 -2980.5435 0.76893619 0.59126286 1.1646672 0.27529682
3500 281.19 -1143.0785 -2979.8374 -2980.6693 0.54860209 0.30096426 0.79069857 -0.36626891
3600 296.58287 1156.4706 -2979.2182 -2980.6646 0.55745952 0.31076112 0.81914175 -0.31895116
3700 297.24517 -1888.4993 -2978.5352 -2980.5318 0.77195451 0.59591377 1.0713124 -0.027796216
3800 290.81586 3843.3483 -2977.8509 -2980.2819 1.0444771 1.0909324 0.88270245 -0.57339499
3900 300.39456 -5584.8386 -2977.0837 -2979.9273 1.3073719 1.7092212 0.65444496 -0.94023014
4000 306.15811 3310.0105 -2976.5086 -2979.4859 1.5269967 2.3317191 0.45120199 -1.1665402
4100 295.907 -1475.0458 -2975.9096 -2978.9779 1.6878413 2.8488082 0.27738537 -1.2909517
4200 322.70162 933.76586 -2975.3867 -2978.425 1.7872637 3.1943116 0.12322364 -1.3421568
4300 306.69631 -512.7048 -2974.9324 -2977.8465 1.8221493 3.3202281 -0.016769435 -1.3380921
4400 309.23776 226.77219 -2974.5791 -2977.2621 1.788532 3.1988469 -0.14279249 -1.3044784
4500 313.15783 508.29785 -2974.3263 -2976.6947 1.6959722 2.8763217 -0.26351575 -1.2425552
4600 316.26151 -2043.7571 -2974.1697 -2976.1635 1.5525328 2.4103582 -0.38443906 -1.156175
4700 312.27329 1831.682 -2974.1732 -2975.6917 1.3614048 1.8534231 -0.52504872 -1.0383081
4800 307.61066 -1476.0019 -2974.2885 -2975.296 1.1354139 1.2891647 -0.69734331 -0.84719677
4900 305.73489 1303.4848 -2974.5506 -2974.9905 0.8913743 0.79454814 -0.90609876 -0.50216921
5000 309.3774 -1574.6812 -2974.8687 -2974.7812 0.65272109 0.42604482 -1.0613188 0.00291608
5100 304.8602 2679.7476 -2975.3082 -2974.6718 0.4727141 0.22345862 -0.75321909 -0.42028824
5200 297.54226 -5008.0905 -2975.7443 -2974.6646 0.45797515 0.20974124 -0.66557441 -0.64583954
5300 306.18872 4840.4175 -2976.324 -2974.7575 0.61348896 0.3763687 -1.0084709 -0.10258503
5400 299.57661 -2513.1706 -2976.8842 -2974.9472 0.83376011 0.69515592 -0.88189118 -0.55222188
5500 302.30844 1301.3525 -2977.4539 -2975.2244 1.0486412 1.0996484 -0.65075151 -0.94687541
5600 302.11038 -760.79712 -2977.9764 -2975.5765 1.2259535 1.502962 -0.44510538 -1.1709493
5700 294.49825 718.67318 -2978.4584 -2975.9844 1.357155 1.8418697 -0.27309672 -1.2848748
5800 305.97636 -478.64224 -2978.8638 -2976.429 1.4331646 2.0539608 -0.1197893 -1.3417863
5900 291.93868 -419.74179 -2979.2292 -2976.8905 1.4535887 2.1129201 0.024018983 -1.349863
6000 289.50667 859.85085 -2979.5018 -2977.3557 1.4249736 2.0305497 0.15271261 -1.3095465
6100 305.70118 -933.35917 -2979.6877 -2977.8064 1.3480601 1.8172659 0.27785119 -1.2402584
6200 284.37805 1526.0707 -2979.806 -2978.2265 1.2296781 1.5121082 0.40681415 -1.1355005
6300 291.08863 -2156.6708 -2979.8064 -2978.6017 1.0733214 1.1520189 0.54137333 -1.0156432
6400 295.99073 2819.8245 -2979.7378 -2978.9165 0.8941904 0.79957647 0.7073501 -0.82385123
6500 298.06769 -3396.3504 -2979.5428 -2979.1626 0.70228297 0.49320137 0.91043588 -0.48653641
6600 301.78514 5496.6525 -2979.2768 -2979.3329 0.51276653 0.26292952 1.0681056 -0.036293782
6700 290.80665 -5229.4989 -2978.9177 -2979.4217 0.36990055 0.13682642 0.81466085 -0.37332419
6800 296.75761 2401.7807 -2978.5996 -2979.4338 0.34589164 0.11964103 0.65253856 -0.7737558
6900 295.77553 -1521.6269 -2978.1619 -2979.3685 0.46007271 0.21166689 1.0427138 -0.013014477
7000 303.59015 1530.7255 -2977.7097 -2979.225 0.63320287 0.40094588 0.93012255 -0.45527217
7100 297.51038 -3016.4426 -2977.2025 -2979.0103 0.81101521 0.65774567 0.7114444 -0.84465178
7200 293.53789 2705.9808 -2976.7651 -2978.7294 0.97512025 0.95085951 0.52979295 -1.0479526
7300 301.78809 -1042.1076 -2976.3388 -2978.3998 1.1024575 1.2154126 0.35564664 -1.2137023
7400 307.50053 214.56923 -2975.9581 -2978.0341 1.188001 1.4113463 0.20025025 -1.3077784
7500 301.98985 281.86495 -2975.6146 -2977.6451 1.2301918 1.5133718 0.063886193 -1.3465506
7600 318.37347 -1145.7795 -2975.3473 -2977.2486 1.2295055 1.5116837 -0.066939137 -1.3475567
7700 314.94512 4536.9887 -2975.1351 -2976.8564 1.1948121 1.427576 -0.19450637 -1.2864658
7800 312.91485 -2980.6408 -2975.0156 -2976.4828 1.1134406 1.2397499 -0.32749726 -1.207718
7900 310.06854 2244.3877 -2975.0094 -2976.1462 0.99080702 0.98169854 -0.48336959 -1.0840695
8000 308.55007 -2427.1464 -2975.0491 -2975.8566 0.83800849 0.70225823 -0.65822117 -0.89212512
8100 323.02796 3187.4728 -2975.2081 -2975.6251 0.66510054 0.44235872 -0.84857729 -0.62984027
8200 327.05029 -6447.7875 -2975.3162 -2975.4608 0.49730291 0.24731018 -1.0534735 -0.14095413
8300 311.194 4273.1174 -2975.7217 -2975.3642 0.35491458 0.12596436 -0.95967595 -0.04445204
8400 290.61931 -2301.019 -2976.0963 -2975.3446 0.31530296 0.09941596 -0.69056625 -0.72257435
8500 314.00559 1966.1297 -2976.5206 -2975.3995 0.41659574 0.17355201 -1.1134124 0.18107632
8600 288.26541 -1608.4524 -2976.9304 -2975.526 0.57968749 0.33603759 -1.0014591 -0.34698354
8700 298.92083 1353.9988 -2977.355 -2975.7203 0.74176087 0.55020919 -0.74109062 -0.86227705
8800 299.97274 -638.68301 -2977.766 -2975.9682 0.87950613 0.77353104 -0.50839929 -1.1555064
8900 300.66443 -279.62514 -2978.1476 -2976.262 0.99526406 0.99055054 -0.33059914 -1.261881
9000 290.44715 489.06352 -2978.4892 -2976.5918 1.0763797 1.1585932 -0.17871557 -1.3082755
9100 289.06733 -1063.4482 -2978.784 -2976.943 1.1174524 1.2486999 -0.037767225 -1.3120851
9200 297.63931 2664.6535 -2979.0202 -2977.3033 1.1127042 1.2381106 0.090936095 -1.2913777
9300 297.9983 -4684.428 -2979.1316 -2977.6563 1.0596342 1.1228247 0.20756305 -1.2867214
9400 285.14009 2779.1548 -2979.2804 -2977.9868 0.98034602 0.96107833 0.33668495 -1.2294268
9500 284.11569 -2437.5003 -2979.2918 -2978.2852 0.87286876 0.76189987 0.48407552 -1.1274969
9600 291.97193 2772.1396 -2979.2473 -2978.5402 0.74294711 0.55197041 0.67450455 -0.91152584
9700 292.59563 -3615.4496 -2979.0801 -2978.7442 0.59448857 0.35341666 0.91630006 -0.47180257
9800 296.1785 4869.2744 -2978.8849 -2978.891 0.43463281 0.18890568 1.1020846 0.093881572
9900 298.44745 -3587.7391 -2978.5978 -2978.9712 0.30680426 0.094128854 0.8532075 -0.19634913
10000 297.99863 1312.5643 -2978.3205 -2978.9854 0.27829395 0.077447522 0.60818263 -0.79004935
Loop time of 15.3108 on 4 procs for 10000 steps with 864 atoms
Performance: 112.862 ns/day, 0.213 hours/ns, 653.136 timesteps/s, 564.309 katom-step/s
92.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.428 | 12.158 | 12.621 | 13.0 | 79.41
Neigh | 0.0019158 | 0.0020708 | 0.002163 | 0.2 | 0.01
Comm | 1.936 | 2.3948 | 3.0967 | 28.3 | 15.64
Output | 0.0026067 | 0.0037308 | 0.0066123 | 2.7 | 0.02
Modify | 0.44688 | 0.45929 | 0.47131 | 1.6 | 3.00
Other | | 0.2928 | | | 1.91
Nlocal: 216 ave 224 max 204 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Nghost: 2147 ave 2159 max 2139 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 24185.8 ave 26045 max 21309 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 96743
Ave neighs/atom = 111.97106
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:15

178
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LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# create pure copper system
units metal
lattice fcc 3.75
Lattice spacing in x,y,z = 3.75 3.75 3.75
region box block 0 6 0 6 0 6
create_box 2 box
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
1 by 1 by 1 MPI processor grid
timestep 0.002
create_atoms 1 box
Created 864 atoms
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
create_atoms CPU = 0.001 seconds
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# Initialize to a high temperature, then cool in npt ensemble
velocity all create 1000.0 6567345
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
variable toteng equal "etotal"
fix 2 all ave/moments 1 10 10 v_toteng mean variance skew kurtosis
thermo_style custom step etotal f_2[*]
thermo_modify format float %14.8f
thermo 1
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, 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) = 3.484 | 3.484 | 3.484 Mbytes
Step TotEng f_2[1] f_2[2] f_2[3] f_2[4]
0 -2884.91592826 0.00000000 0.00000000 0.00000000 0.00000000
1 -2888.74461907 0.00000000 0.00000000 0.00000000 0.00000000
2 -2898.78491936 0.00000000 0.00000000 0.00000000 0.00000000
3 -2910.70619667 0.00000000 0.00000000 0.00000000 0.00000000
4 -2919.41734302 0.00000000 0.00000000 0.00000000 0.00000000
5 -2923.24980175 0.00000000 0.00000000 0.00000000 0.00000000
6 -2923.79800148 0.00000000 0.00000000 0.00000000 0.00000000
7 -2922.97580252 0.00000000 0.00000000 0.00000000 0.00000000
8 -2921.95601941 0.00000000 0.00000000 0.00000000 0.00000000
9 -2921.45319499 0.00000000 0.00000000 0.00000000 0.00000000
10 -2921.81460149 -2915.29004998 148.32538381 1.60272422 1.50844200
11 -2923.00059466 -2915.29004998 148.32538381 1.60272422 1.50844200
12 -2924.63075671 -2915.29004998 148.32538381 1.60272422 1.50844200
13 -2926.18037946 -2915.29004998 148.32538381 1.60272422 1.50844200
14 -2927.22356281 -2915.29004998 148.32538381 1.60272422 1.50844200
15 -2927.62053073 -2915.29004998 148.32538381 1.60272422 1.50844200
16 -2927.49949128 -2915.29004998 148.32538381 1.60272422 1.50844200
17 -2927.12292174 -2915.29004998 148.32538381 1.60272422 1.50844200
18 -2926.73637250 -2915.29004998 148.32538381 1.60272422 1.50844200
19 -2926.49482990 -2915.29004998 148.32538381 1.60272422 1.50844200
20 -2926.44714720 -2926.29565870 2.07215006 1.62317861 2.37019300
21 -2926.56102718 -2926.29565870 2.07215006 1.62317861 2.37019300
22 -2926.76734347 -2926.29565870 2.07215006 1.62317861 2.37019300
23 -2926.98403044 -2926.29565870 2.07215006 1.62317861 2.37019300
24 -2927.15193693 -2926.29565870 2.07215006 1.62317861 2.37019300
25 -2927.24498540 -2926.29565870 2.07215006 1.62317861 2.37019300
26 -2927.26914121 -2926.29565870 2.07215006 1.62317861 2.37019300
27 -2927.25021402 -2926.29565870 2.07215006 1.62317861 2.37019300
28 -2927.21637817 -2926.29565870 2.07215006 1.62317861 2.37019300
29 -2927.19085616 -2926.29565870 2.07215006 1.62317861 2.37019300
30 -2927.18360687 -2927.08195198 0.05722486 1.54894969 1.44984748
31 -2927.19243579 -2927.08195198 0.05722486 1.54894969 1.44984748
32 -2927.20805612 -2927.08195198 0.05722486 1.54894969 1.44984748
33 -2927.22285606 -2927.08195198 0.05722486 1.54894969 1.44984748
34 -2927.23274852 -2927.08195198 0.05722486 1.54894969 1.44984748
35 -2927.23953263 -2927.08195198 0.05722486 1.54894969 1.44984748
36 -2927.24805761 -2927.08195198 0.05722486 1.54894969 1.44984748
37 -2927.26215638 -2927.08195198 0.05722486 1.54894969 1.44984748
38 -2927.28298252 -2927.08195198 0.05722486 1.54894969 1.44984748
39 -2927.31025065 -2927.08195198 0.05722486 1.54894969 1.44984748
40 -2927.33874897 -2927.25378252 0.00209108 -0.65432756 -0.21113798
41 -2927.36224413 -2927.25378252 0.00209108 -0.65432756 -0.21113798
42 -2927.37729800 -2927.25378252 0.00209108 -0.65432756 -0.21113798
43 -2927.38671916 -2927.25378252 0.00209108 -0.65432756 -0.21113798
44 -2927.39115082 -2927.25378252 0.00209108 -0.65432756 -0.21113798
45 -2927.39614318 -2927.25378252 0.00209108 -0.65432756 -0.21113798
46 -2927.40444730 -2927.25378252 0.00209108 -0.65432756 -0.21113798
47 -2927.41888601 -2927.25378252 0.00209108 -0.65432756 -0.21113798
48 -2927.43954388 -2927.25378252 0.00209108 -0.65432756 -0.21113798
49 -2927.46210058 -2927.25378252 0.00209108 -0.65432756 -0.21113798
50 -2927.48270024 -2927.41212333 0.00148630 -0.72914987 -0.39161968
51 -2927.49822500 -2927.41212333 0.00148630 -0.72914987 -0.39161968
52 -2927.50765361 -2927.41212333 0.00148630 -0.72914987 -0.39161968
53 -2927.51223225 -2927.41212333 0.00148630 -0.72914987 -0.39161968
54 -2927.51510653 -2927.41212333 0.00148630 -0.72914987 -0.39161968
55 -2927.52035921 -2927.41212333 0.00148630 -0.72914987 -0.39161968
56 -2927.53170012 -2927.41212333 0.00148630 -0.72914987 -0.39161968
57 -2927.54910408 -2927.41212333 0.00148630 -0.72914987 -0.39161968
58 -2927.57357292 -2927.41212333 0.00148630 -0.72914987 -0.39161968
59 -2927.60356966 -2927.41212333 0.00148630 -0.72914987 -0.39161968
60 -2927.63344447 -2927.54449679 0.00204640 -1.06571776 0.04430271
61 -2927.66186165 -2927.54449679 0.00204640 -1.06571776 0.04430271
62 -2927.68810360 -2927.54449679 0.00204640 -1.06571776 0.04430271
63 -2927.71163480 -2927.54449679 0.00204640 -1.06571776 0.04430271
64 -2927.73036225 -2927.54449679 0.00204640 -1.06571776 0.04430271
65 -2927.74726656 -2927.54449679 0.00204640 -1.06571776 0.04430271
66 -2927.76525638 -2927.54449679 0.00204640 -1.06571776 0.04430271
67 -2927.78432762 -2927.54449679 0.00204640 -1.06571776 0.04430271
68 -2927.80305095 -2927.54449679 0.00204640 -1.06571776 0.04430271
69 -2927.82406714 -2927.54449679 0.00204640 -1.06571776 0.04430271
70 -2927.84622122 -2927.75621522 0.00356092 0.06232090 -0.94076248
71 -2927.86886493 -2927.75621522 0.00356092 0.06232090 -0.94076248
72 -2927.89150302 -2927.75621522 0.00356092 0.06232090 -0.94076248
73 -2927.91480122 -2927.75621522 0.00356092 0.06232090 -0.94076248
74 -2927.93739399 -2927.75621522 0.00356092 0.06232090 -0.94076248
75 -2927.96075707 -2927.75621522 0.00356092 0.06232090 -0.94076248
76 -2927.98525702 -2927.75621522 0.00356092 0.06232090 -0.94076248
77 -2928.00918972 -2927.75621522 0.00356092 0.06232090 -0.94076248
78 -2928.03266453 -2927.75621522 0.00356092 0.06232090 -0.94076248
79 -2928.05673430 -2927.75621522 0.00356092 0.06232090 -0.94076248
80 -2928.08120268 -2927.97383685 0.00511363 -0.03242365 -1.20956903
81 -2928.10618717 -2927.97383685 0.00511363 -0.03242365 -1.20956903
82 -2928.13191751 -2927.97383685 0.00511363 -0.03242365 -1.20956903
83 -2928.15675025 -2927.97383685 0.00511363 -0.03242365 -1.20956903
84 -2928.18178044 -2927.97383685 0.00511363 -0.03242365 -1.20956903
85 -2928.20538210 -2927.97383685 0.00511363 -0.03242365 -1.20956903
86 -2928.22991006 -2927.97383685 0.00511363 -0.03242365 -1.20956903
87 -2928.25238345 -2927.97383685 0.00511363 -0.03242365 -1.20956903
88 -2928.27490378 -2927.97383685 0.00511363 -0.03242365 -1.20956903
89 -2928.29697980 -2927.97383685 0.00511363 -0.03242365 -1.20956903
90 -2928.31902032 -2928.21552149 0.00511983 0.08421866 -1.19120544
91 -2928.34079951 -2928.21552149 0.00511983 0.08421866 -1.19120544
92 -2928.36448072 -2928.21552149 0.00511983 0.08421866 -1.19120544
93 -2928.38918869 -2928.21552149 0.00511983 0.08421866 -1.19120544
94 -2928.41578734 -2928.21552149 0.00511983 0.08421866 -1.19120544
95 -2928.44466633 -2928.21552149 0.00511983 0.08421866 -1.19120544
96 -2928.47414034 -2928.21552149 0.00511983 0.08421866 -1.19120544
97 -2928.50507273 -2928.21552149 0.00511983 0.08421866 -1.19120544
98 -2928.53751007 -2928.21552149 0.00511983 0.08421866 -1.19120544
99 -2928.56947939 -2928.21552149 0.00511983 0.08421866 -1.19120544
100 -2928.60000318 -2928.46411283 0.00779929 -0.14908790 -1.24292534
Loop time of 0.579661 on 1 procs for 100 steps with 864 atoms
Performance: 29.811 ns/day, 0.805 hours/ns, 172.515 timesteps/s, 149.053 katom-step/s
96.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.54316 | 0.54316 | 0.54316 | 0.0 | 93.70
Neigh | 0.0041212 | 0.0041212 | 0.0041212 | 0.0 | 0.71
Comm | 0.0034702 | 0.0034702 | 0.0034702 | 0.0 | 0.60
Output | 0.014085 | 0.014085 | 0.014085 | 0.0 | 2.43
Modify | 0.01321 | 0.01321 | 0.01321 | 0.0 | 2.28
Other | | 0.001612 | | | 0.28
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3767 ave 3767 max 3767 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 96746 ave 96746 max 96746 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 96746
Ave neighs/atom = 111.97454
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

178
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LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# create pure copper system
units metal
lattice fcc 3.75
Lattice spacing in x,y,z = 3.75 3.75 3.75
region box block 0 6 0 6 0 6
create_box 2 box
Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
1 by 2 by 2 MPI processor grid
timestep 0.002
create_atoms 1 box
Created 864 atoms
using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
create_atoms CPU = 0.001 seconds
pair_style eam/alloy
pair_coeff * * AlCu.eam.alloy Cu Al
# Initialize to a high temperature, then cool in npt ensemble
velocity all create 1000.0 6567345
fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
variable toteng equal "etotal"
fix 2 all ave/moments 1 10 10 v_toteng mean variance skew kurtosis
thermo_style custom step etotal f_2[*]
thermo_modify format float %14.8f
thermo 1
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, 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) = 3.42 | 3.42 | 3.42 Mbytes
Step TotEng f_2[1] f_2[2] f_2[3] f_2[4]
0 -2884.91592826 0.00000000 0.00000000 0.00000000 0.00000000
1 -2888.74473521 0.00000000 0.00000000 0.00000000 0.00000000
2 -2898.78463435 0.00000000 0.00000000 0.00000000 0.00000000
3 -2910.70366466 0.00000000 0.00000000 0.00000000 0.00000000
4 -2919.40999553 0.00000000 0.00000000 0.00000000 0.00000000
5 -2923.23570887 0.00000000 0.00000000 0.00000000 0.00000000
6 -2923.77707961 0.00000000 0.00000000 0.00000000 0.00000000
7 -2922.94386730 0.00000000 0.00000000 0.00000000 0.00000000
8 -2921.92251474 0.00000000 0.00000000 0.00000000 0.00000000
9 -2921.42476103 0.00000000 0.00000000 0.00000000 0.00000000
10 -2921.79501042 -2915.27419717 148.08574615 1.60354430 1.51194865
11 -2922.99498349 -2915.27419717 148.08574615 1.60354430 1.51194865
12 -2924.64023395 -2915.27419717 148.08574615 1.60354430 1.51194865
13 -2926.19980790 -2915.27419717 148.08574615 1.60354430 1.51194865
14 -2927.25022454 -2915.27419717 148.08574615 1.60354430 1.51194865
15 -2927.64953875 -2915.27419717 148.08574615 1.60354430 1.51194865
16 -2927.52804735 -2915.27419717 148.08574615 1.60354430 1.51194865
17 -2927.14916045 -2915.27419717 148.08574615 1.60354430 1.51194865
18 -2926.76078244 -2915.27419717 148.08574615 1.60354430 1.51194865
19 -2926.51878380 -2915.27419717 148.08574615 1.60354430 1.51194865
20 -2926.47129883 -2926.31628615 2.10313655 1.62594474 2.38000930
21 -2926.59030835 -2926.31628615 2.10313655 1.62594474 2.38000930
22 -2926.80121221 -2926.31628615 2.10313655 1.62594474 2.38000930
23 -2927.02526150 -2926.31628615 2.10313655 1.62594474 2.38000930
24 -2927.20079704 -2926.31628615 2.10313655 1.62594474 2.38000930
25 -2927.30192483 -2926.31628615 2.10313655 1.62594474 2.38000930
26 -2927.33194351 -2926.31628615 2.10313655 1.62594474 2.38000930
27 -2927.31647527 -2926.31628615 2.10313655 1.62594474 2.38000930
28 -2927.28391864 -2926.31628615 2.10313655 1.62594474 2.38000930
29 -2927.25821953 -2926.31628615 2.10313655 1.62594474 2.38000930
30 -2927.25085808 -2927.13609190 0.06387000 1.52055179 1.31247839
31 -2927.25723201 -2927.13609190 0.06387000 1.52055179 1.31247839
32 -2927.27197789 -2927.13609190 0.06387000 1.52055179 1.31247839
33 -2927.28667044 -2927.13609190 0.06387000 1.52055179 1.31247839
34 -2927.29879455 -2927.13609190 0.06387000 1.52055179 1.31247839
35 -2927.30701891 -2927.13609190 0.06387000 1.52055179 1.31247839
36 -2927.31785921 -2927.13609190 0.06387000 1.52055179 1.31247839
37 -2927.33272014 -2927.13609190 0.06387000 1.52055179 1.31247839
38 -2927.35282056 -2927.13609190 0.06387000 1.52055179 1.31247839
39 -2927.37849130 -2927.13609190 0.06387000 1.52055179 1.31247839
40 -2927.40448350 -2927.32080685 0.00219675 -0.52051260 -0.50322958
41 -2927.42423249 -2927.32080685 0.00219675 -0.52051260 -0.50322958
42 -2927.43769919 -2927.32080685 0.00219675 -0.52051260 -0.50322958
43 -2927.44493813 -2927.32080685 0.00219675 -0.52051260 -0.50322958
44 -2927.44923137 -2927.32080685 0.00219675 -0.52051260 -0.50322958
45 -2927.45439729 -2927.32080685 0.00219675 -0.52051260 -0.50322958
46 -2927.46365674 -2927.32080685 0.00219675 -0.52051260 -0.50322958
47 -2927.48173952 -2927.32080685 0.00219675 -0.52051260 -0.50322958
48 -2927.50371663 -2927.32080685 0.00219675 -0.52051260 -0.50322958
49 -2927.52750629 -2927.32080685 0.00219675 -0.52051260 -0.50322958
50 -2927.54872274 -2927.47358404 0.00168128 -0.79883601 -0.48497973
51 -2927.56277664 -2927.47358404 0.00168128 -0.79883601 -0.48497973
52 -2927.57050508 -2927.47358404 0.00168128 -0.79883601 -0.48497973
53 -2927.57241043 -2927.47358404 0.00168128 -0.79883601 -0.48497973
54 -2927.57517748 -2927.47358404 0.00168128 -0.79883601 -0.48497973
55 -2927.58161786 -2927.47358404 0.00168128 -0.79883601 -0.48497973
56 -2927.59393740 -2927.47358404 0.00168128 -0.79883601 -0.48497973
57 -2927.61367876 -2927.47358404 0.00168128 -0.79883601 -0.48497973
58 -2927.64096296 -2927.47358404 0.00168128 -0.79883601 -0.48497973
59 -2927.67356621 -2927.47358404 0.00168128 -0.79883601 -0.48497973
60 -2927.70625176 -2927.60908846 0.00241645 -1.10903745 0.07175615
61 -2927.73673853 -2927.60908846 0.00241645 -1.10903745 0.07175615
62 -2927.76292153 -2927.60908846 0.00241645 -1.10903745 0.07175615
63 -2927.78541405 -2927.60908846 0.00241645 -1.10903745 0.07175615
64 -2927.80292853 -2927.60908846 0.00241645 -1.10903745 0.07175615
65 -2927.81988675 -2927.60908846 0.00241645 -1.10903745 0.07175615
66 -2927.83680256 -2927.60908846 0.00241645 -1.10903745 0.07175615
67 -2927.85379296 -2927.60908846 0.00241645 -1.10903745 0.07175615
68 -2927.87418119 -2927.60908846 0.00241645 -1.10903745 0.07175615
69 -2927.89451588 -2927.60908846 0.00241645 -1.10903745 0.07175615
70 -2927.91602570 -2927.82832077 0.00334657 0.04700770 -0.91589129
71 -2927.93874793 -2927.82832077 0.00334657 0.04700770 -0.91589129
72 -2927.96195498 -2927.82832077 0.00334657 0.04700770 -0.91589129
73 -2927.98521535 -2927.82832077 0.00334657 0.04700770 -0.91589129
74 -2928.01060565 -2927.82832077 0.00334657 0.04700770 -0.91589129
75 -2928.03584561 -2927.82832077 0.00334657 0.04700770 -0.91589129
76 -2928.06090892 -2927.82832077 0.00334657 0.04700770 -0.91589129
77 -2928.08509438 -2927.82832077 0.00334657 0.04700770 -0.91589129
78 -2928.11095399 -2927.82832077 0.00334657 0.04700770 -0.91589129
79 -2928.13711339 -2927.82832077 0.00334657 0.04700770 -0.91589129
80 -2928.16413424 -2928.04905744 0.00575008 -0.05409710 -1.19501222
81 -2928.19005959 -2928.04905744 0.00575008 -0.05409710 -1.19501222
82 -2928.21654649 -2928.04905744 0.00575008 -0.05409710 -1.19501222
83 -2928.24249986 -2928.04905744 0.00575008 -0.05409710 -1.19501222
84 -2928.26861892 -2928.04905744 0.00575008 -0.05409710 -1.19501222
85 -2928.29480718 -2928.04905744 0.00575008 -0.05409710 -1.19501222
86 -2928.32144325 -2928.04905744 0.00575008 -0.05409710 -1.19501222
87 -2928.34727619 -2928.04905744 0.00575008 -0.05409710 -1.19501222
88 -2928.37131285 -2928.04905744 0.00575008 -0.05409710 -1.19501222
89 -2928.39531126 -2928.04905744 0.00575008 -0.05409710 -1.19501222
90 -2928.41739503 -2928.30652706 0.00595440 0.06693205 -1.24851322
91 -2928.43978811 -2928.30652706 0.00595440 0.06693205 -1.24851322
92 -2928.46316822 -2928.30652706 0.00595440 0.06693205 -1.24851322
93 -2928.48654219 -2928.30652706 0.00595440 0.06693205 -1.24851322
94 -2928.51132482 -2928.30652706 0.00595440 0.06693205 -1.24851322
95 -2928.53938009 -2928.30652706 0.00595440 0.06693205 -1.24851322
96 -2928.56852408 -2928.30652706 0.00595440 0.06693205 -1.24851322
97 -2928.59814410 -2928.30652706 0.00595440 0.06693205 -1.24851322
98 -2928.62787940 -2928.30652706 0.00595440 0.06693205 -1.24851322
99 -2928.65853178 -2928.30652706 0.00595440 0.06693205 -1.24851322
100 -2928.68735978 -2928.55806426 0.00711607 -0.13829819 -1.25519738
Loop time of 0.327437 on 4 procs for 100 steps with 864 atoms
Performance: 52.774 ns/day, 0.455 hours/ns, 305.402 timesteps/s, 263.868 katom-step/s
91.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.27213 | 0.27259 | 0.27312 | 0.1 | 83.25
Neigh | 0.00096945 | 0.0015991 | 0.0022533 | 1.5 | 0.49
Comm | 0.026726 | 0.027088 | 0.027516 | 0.2 | 8.27
Output | 0.0029839 | 0.0048706 | 0.0097487 | 4.0 | 1.49
Modify | 0.012374 | 0.016834 | 0.018623 | 2.0 | 5.14
Other | | 0.004455 | | | 1.36
Nlocal: 216 ave 224 max 204 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Nghost: 2147 ave 2159 max 2139 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 24185.8 ave 26045 max 21309 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 96743
Ave neighs/atom = 111.97106
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

1
examples/PACKAGES/neighbor-swap/MoCoNiVFeAlCr_2nn.meam Symbolic link
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../../../potentials/MoCoNiVFeAlCr_2nn.meam

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examples/PACKAGES/neighbor-swap/in.KMC_pulse_center Normal file
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# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
create_atoms 1 region whole
replicate 6 16 6
region puck block INF INF 7 9 INF INF
set region puck type 2
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124 loop geom
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
#write_data pulse_center.data

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examples/PACKAGES/neighbor-swap/in.KMC_pulse_edge Normal file
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# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
create_atoms 1 region whole
replicate 6 16 6
region puck block INF INF INF 2 INF INF
set region puck type 2
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124 loop geom
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
#write_data pulse_end.data

1
examples/PACKAGES/neighbor-swap/library_2nn.meam Symbolic link
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../../../potentials/library_2nn.meam

154
examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_center.g++.1 Normal file
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
1 by 1 by 1 MPI processor grid
create_atoms 1 region whole
Created 4 atoms
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
create_atoms CPU = 0.000 seconds
replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
1 by 1 by 1 MPI processor grid
2304 atoms
replicate CPU = 0.000 seconds
region puck block INF INF 7 9 INF INF
set region puck type 2
Setting atom values ...
360 settings made for type
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 18 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -9674.3728 0 -9674.3728 -212400.94
Loop time of 1.202e-06 on 1 procs for 0 steps with 2304 atoms
0.0% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.202e-06 | | |100.00
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4735 ave 4735 max 4735 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99072 ave 99072 max 99072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 198144 ave 198144 max 198144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
0 2400 -187517.52 -187403.07 -187750.14 -187399.35 22.572 60.192 22.572 30667.534 -9674.3728 0 0
100 1664.9956 14000 14280.682 15095.077 12624.241 21.635315 57.726568 21.64791 27036.778 -9592.8978 24 22
200 1560.0093 -5452.2434 -5749.5816 -2957.4228 -7649.7258 21.734212 58.085959 21.724853 27426.596 -9562.8822 48 45
300 1586.4553 2030.9253 2776.4677 775.50538 2540.803 21.678654 58.101753 21.654423 27275.215 -9571.1308 72 66
400 1603.6896 -223.16773 156.17673 -478.47929 -347.20061 21.701021 58.098904 21.657752 27306.213 -9576.4456 96 90
500 1618.236 -925.51874 -1640.9078 451.6228 -1587.2713 21.718334 58.042685 21.666081 27312.054 -9581.2045 120 110
600 1581.9995 290.10126 1359.1314 1407.5434 -1896.371 21.679813 58.086147 21.692118 27316.815 -9570.4803 144 132
700 1568.3261 1387.3472 938.81523 2159.3686 1063.8577 21.685928 58.075626 21.67273 27295.153 -9566.2914 168 155
800 1607.1531 46.792964 -453.90265 -1533.3908 2127.6723 21.685188 58.202356 21.628338 27297.753 -9577.7848 192 177
900 1573.4747 -84.225488 548.90935 -1356.7479 555.16208 21.69634 58.150052 21.651847 27316.908 -9567.7039 216 196
1000 1609.2136 1215.0833 764.08936 3301.0811 -419.92053 21.683731 58.000401 21.68726 27275.31 -9578.2843 240 219
Loop time of 31.6263 on 1 procs for 1000 steps with 2304 atoms
Performance: 5.464 ns/day, 4.393 hours/ns, 31.619 timesteps/s, 72.851 katom-step/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.487 | 28.487 | 28.487 | 0.0 | 90.07
Neigh | 0.22789 | 0.22789 | 0.22789 | 0.0 | 0.72
Comm | 0.010808 | 0.010808 | 0.010808 | 0.0 | 0.03
Output | 0.00033526 | 0.00033526 | 0.00033526 | 0.0 | 0.00
Modify | 2.8963 | 2.8963 | 2.8963 | 0.0 | 9.16
Other | | 0.003905 | | | 0.01
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4750 ave 4750 max 4750 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 130023 ave 130023 max 130023 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 260046 ave 260046 max 260046 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 260046
Ave neighs/atom = 112.86719
Neighbor list builds = 65
Dangerous builds = 0
#write_data pulse_center.data
Total wall time: 0:00:31

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examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_center.g++.4 Normal file
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
1 by 2 by 2 MPI processor grid
create_atoms 1 region whole
Created 4 atoms
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
create_atoms CPU = 0.000 seconds
replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
1 by 4 by 1 MPI processor grid
2304 atoms
replicate CPU = 0.000 seconds
region puck block INF INF 7 9 INF INF
set region puck type 2
Setting atom values ...
360 settings made for type
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 18 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -9674.3728 0 -9674.3728 -212400.94
Loop time of 1.422e-06 on 4 procs for 0 steps with 2304 atoms
35.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.422e-06 | | |100.00
Nlocal: 576 ave 576 max 576 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2131 ave 2131 max 2131 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 24768 ave 24768 max 24768 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 49536 ave 49536 max 49536 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
0 2400 -187517.52 -187403.09 -187750.05 -187399.42 22.572 60.192 22.572 30667.534 -9674.3728 0 0
100 1668.8754 13300.763 12419.304 15568.772 11914.212 21.636248 57.724775 21.647685 27036.823 -9594.7526 24 23
200 1584.9699 -5686.0414 -4741.8496 -5914.7681 -6401.5064 21.729384 58.060532 21.730736 27415.923 -9571.0639 48 46
300 1582.0473 2806.2983 3413.4122 2716.0124 2289.4702 21.6679 58.033587 21.694744 27280.402 -9570.5549 72 69
400 1582.5825 845.29268 -849.61221 2123.5339 1261.9563 21.676298 58.14253 21.656418 27293.905 -9570.7948 96 93
500 1591.7285 -501.17955 1151.9743 -1719.3712 -936.14174 21.696367 58.157211 21.648308 27315.839 -9573.5089 120 116
600 1610.708 -821.74669 -1002.4957 291.88502 -1754.6294 21.730338 58.008213 21.661226 27304.8 -9579.5573 144 138
700 1598.5176 -590.00633 -1844.42 408.97706 -334.57602 21.712908 57.96131 21.698129 27307.281 -9575.8973 168 162
800 1584.3478 330.16711 666.88818 74.698331 248.91482 21.650908 58.045055 21.719838 27295.933 -9571.9268 192 186
900 1557.9946 1471.1207 2124.6512 1526.9937 761.71731 21.645578 58.156083 21.681637 27293.323 -9564.4385 216 207
1000 1582.5312 379.57005 -602.96446 2696.737 -955.06238 21.655418 58.231248 21.649581 27300.598 -9571.9879 240 227
Loop time of 9.1632 on 4 procs for 1000 steps with 2304 atoms
Performance: 18.858 ns/day, 1.273 hours/ns, 109.132 timesteps/s, 251.440 katom-step/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.867 | 7.9923 | 8.1311 | 4.3 | 87.22
Neigh | 0.054997 | 0.057518 | 0.060145 | 1.0 | 0.63
Comm | 0.017529 | 0.14801 | 0.27408 | 29.5 | 1.62
Output | 0.00015963 | 0.00017216 | 0.00020869 | 0.0 | 0.00
Modify | 0.95227 | 0.96325 | 0.9917 | 1.7 | 10.51
Other | | 0.001983 | | | 0.02
Nlocal: 576 ave 609 max 540 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2161.5 ave 2173 max 2151 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 32450.2 ave 35422 max 29271 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 64900.5 ave 70800 max 58684 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 259602
Ave neighs/atom = 112.67448
Neighbor list builds = 62
Dangerous builds = 0
#write_data pulse_center.data
Total wall time: 0:00:09

155
examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_edge.g++.1 Normal file
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
1 by 1 by 1 MPI processor grid
create_atoms 1 region whole
Created 4 atoms
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
create_atoms CPU = 0.000 seconds
replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
1 by 1 by 1 MPI processor grid
2304 atoms
replicate CPU = 0.000 seconds
region puck block INF INF INF 2 INF INF
set region puck type 2
Setting atom values ...
360 settings made for type
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 18 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -9674.3728 0 -9674.3728 -212400.94
Loop time of 1.232e-06 on 1 procs for 0 steps with 2304 atoms
81.2% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.232e-06 | | |100.00
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4735 ave 4735 max 4735 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99072 ave 99072 max 99072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 198144 ave 198144 max 198144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124 loop geom
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
0 2400 -187517.52 -187464.47 -188202.62 -186885.48 22.572 60.192 22.572 30667.534 -9674.3728 0 0
100 1665.6154 14281.316 14426.547 14555.867 13861.534 21.637238 57.719793 21.637281 27022.733 -9594.4303 24 24
200 1603.3309 -7325.7341 -8878.1524 -5333.0485 -7766.0015 21.710246 58.122827 21.725933 27415.106 -9577.4545 48 48
300 1603.2974 207.19165 1983.4565 -1841.9518 480.07024 21.678227 58.079126 21.674033 27288.745 -9577.6391 72 69
400 1600.1515 810.95054 1087.969 802.04946 542.83316 21.683731 58.045848 21.678505 27285.662 -9576.6508 96 92
500 1629.8313 -2808.1005 -3197.9357 310.89931 -5537.265 21.683924 58.090375 21.697076 27330.229 -9585.5435 120 113
600 1598.8232 -67.845623 -1573.0718 -1526.7607 2896.2957 21.70213 58.12191 21.653853 27313.504 -9576.4147 144 137
700 1607.2185 154.66718 -1777.2469 2566.4705 -325.22208 21.712408 57.971553 21.678708 27287.033 -9579.1772 168 158
800 1582.559 -891.23631 -632.46037 -636.88203 -1404.3665 21.671936 58.127004 21.678224 27308.594 -9571.6663 192 180
900 1586.7172 -617.17083 -2495.5378 -2302.8766 2946.9018 21.658489 58.181921 21.668968 27305.771 -9572.9641 216 204
1000 1607.563 -389.8113 810.4908 298.84287 -2278.7676 21.624573 58.076745 21.724272 27283.183 -9579.5034 240 227
Loop time of 31.7733 on 1 procs for 1000 steps with 2304 atoms
Performance: 5.439 ns/day, 4.413 hours/ns, 31.473 timesteps/s, 72.514 katom-step/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.604 | 28.604 | 28.604 | 0.0 | 90.02
Neigh | 0.21293 | 0.21293 | 0.21293 | 0.0 | 0.67
Comm | 0.010645 | 0.010645 | 0.010645 | 0.0 | 0.03
Output | 0.00033194 | 0.00033194 | 0.00033194 | 0.0 | 0.00
Modify | 2.9411 | 2.9411 | 2.9411 | 0.0 | 9.26
Other | | 0.00448 | | | 0.01
Nlocal: 2304 ave 2304 max 2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4748 ave 4748 max 4748 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 130301 ave 130301 max 130301 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 260602 ave 260602 max 260602 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 260602
Ave neighs/atom = 113.10851
Neighbor list builds = 62
Dangerous builds = 0
#write_data pulse_end.data
Total wall time: 0:00:31

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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University
# Initiation -------------------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region whole block 0 1 0 1 0 1
create_box 2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
1 by 2 by 2 MPI processor grid
create_atoms 1 region whole
Created 4 atoms
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
create_atoms CPU = 0.000 seconds
replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
1 by 4 by 1 MPI processor grid
2304 atoms
replicate CPU = 0.000 seconds
region puck block INF INF INF 2 INF INF
set region puck type 2
Setting atom values ...
360 settings made for type
# Force Fields -----------------------------------
pair_style meam
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
# Settings ---------------------------------------
timestep 0.002
thermo 100
# Computations -----------------------------------
compute voroN all voronoi/atom neighbors yes
run 0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 18 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -9674.3728 0 -9674.3728 -212400.94
Loop time of 1.53e-06 on 4 procs for 0 steps with 2304 atoms
65.4% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.53e-06 | | |100.00
Nlocal: 576 ave 576 max 576 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2131 ave 2131 max 2131 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 24768 ave 24768 max 24768 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 49536 ave 49536 max 49536 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
# Execution --------------------------------------
velocity all create 2400 908124 loop geom
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
run 1000
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
0 2400 -187517.52 -187464.47 -188202.62 -186885.48 22.572 60.192 22.572 30667.534 -9674.3728 0 0
100 1665.569 14271.813 14638.855 14316.569 13860.016 21.63675 57.721065 21.637799 27023.366 -9594.291 24 24
200 1598.6479 -6990.8349 -8574.1986 -5033.6147 -7364.6916 21.708963 58.123129 21.724821 27412.223 -9575.7322 48 47
300 1604.388 456.43285 1926.408 -1214.1721 657.0626 21.673369 58.090421 21.671716 27285.018 -9577.698 72 70
400 1601.1591 1303.6721 703.88473 1137.6607 2069.471 21.684004 58.049595 21.671161 27278.522 -9576.4811 96 94
500 1623.6044 -2243.2478 -2084.532 320.87709 -4966.0885 21.686171 58.097101 21.695911 27334.758 -9583.1878 120 118
600 1587.2041 421.60034 190.88741 -328.76599 1402.6796 21.712439 58.086039 21.655927 27312.229 -9572.559 144 141
700 1591.2923 32.327829 -2893.2353 1839.7574 1150.4614 21.719102 57.999862 21.666164 27292.974 -9573.9009 168 165
800 1580.8587 -105.51079 654.26389 -160.04168 -810.75457 21.670225 58.109245 21.684683 27306.229 -9570.6482 192 186
900 1570.7648 1290.088 1252.3689 255.62548 2362.2695 21.68101 58.100507 21.658755 27283.051 -9567.9864 216 209
1000 1598.1483 -125.35291 -3626.5479 3404.789 -154.29983 21.720146 57.952942 21.686111 27297.313 -9576.2975 240 231
Loop time of 9.17241 on 4 procs for 1000 steps with 2304 atoms
Performance: 18.839 ns/day, 1.274 hours/ns, 109.023 timesteps/s, 251.188 katom-step/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7477 | 8.0143 | 8.1344 | 5.5 | 87.37
Neigh | 0.050543 | 0.056882 | 0.05986 | 1.6 | 0.62
Comm | 0.069784 | 0.16898 | 0.40996 | 34.2 | 1.84
Output | 0.00015612 | 0.0001707 | 0.00021249 | 0.0 | 0.00
Modify | 0.90628 | 0.93003 | 0.96157 | 2.2 | 10.14
Other | | 0.002053 | | | 0.02
Nlocal: 576 ave 614 max 505 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2165.75 ave 2204 max 2132 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Neighs: 32430.8 ave 35552 max 26564 min
Histogram: 1 0 0 0 0 0 1 0 0 2
FullNghs: 64861.5 ave 71111 max 53164 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 259446
Ave neighs/atom = 112.60677
Neighbor list builds = 62
Dangerous builds = 0
#write_data pulse_end.data
Total wall time: 0:00:09

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LAMMPS GJ THERMOSTAT EXAMPLE
Required LAMMPS packages: EXTRA-FIX, MOLECULE, EXTRA-PAIR
This directory contains the ingredients to run an NVT simulation using the
GJ thermostats.
Example:
NP=4 #number of processors
mpirun -np $NP lmp_mpi -in.gjf.vhalf
Compared to other thermostats, the GJ thermostat allows for larger timesteps
with the correct Boltzmann statistics. A comparison using averaged properties
from this example's input file is shown below. 'X' denotes a failed simulation.
The theoretical value for KE is 1.1168 eV.
POTENTIAL ENERGY (eV)
| Δt || 0.01 | 0.05 | 0.10 | 0.11 | 0.12 | 0.13 | 0.14 |
|===================||========|========|========|========|========|========|========|
| gjf half || -55.11 | -55.11 | -55.11 | -55.11 | -55.11 | -55.10 | -55.07 |
| gjf full || -55.11 | -55.11 | -55.11 | -55.11 | -55.11 | -55.10 | -55.07 |
| langevin || -55.11 | -55.07 | -54.87 | -54.79 | -54.65 | X | X |
| nvt (Nose-Hoover) || -55.14 | -55.07 | -54.90 | -54.84 | -54.76 | X | X |
|-------------------||--------|--------|--------|--------|--------|--------|--------|
KINETIC ENERGY (eV)
| Δt || 0.01 | 0.05 | 0.10 | 0.11 | 0.12 | 0.13 | 0.14 |
|===================||========|========|========|========|========|========|========|
| gjf half || 1.117 | 1.116 | 1.119 | 1.119 | 1.123 | 1.136 | 1.170 |
| gjf full || 1.116 | 1.071 | 0.938 | 0.898 | 0.858 | 0.817 | 0.780 |
| langevin || 1.110 | 1.113 | 1.121 | 1.129 | 1.157 | X | X |
| nvt (Nose-Hoover) || 1.083 | 1.109 | 1.112 | 1.113 | 1.114 | X | X |
|-------------------||--------|--------|--------|--------|--------|--------|--------|
Script Commands:
--
fix lang all gjf 10 10 1 26488
--
fix lang all gjf 10 10 1 26488 vel vfull
--
fix nve all nve
fix lang all langevin 10 10 1 26488
--
fix noho all nvt temp 10 10 1
--

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# LAMMPS GJF-2GJ THERMOSTAT EXAMPLE
## GJF-2GJ THERMOSTAT
This directory contains the ingredients to run an NVT simulation using the GJF-2GJ thermostat.
Example:
```
NP=4 #number of processors
mpirun -np $NP lmp_mpi -in.gjf.vhalf
```
## Required LAMMPS packages: MOLECULE package

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# GJF-2GJ thermostat
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
include ff-argon.lmp
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vfull
fix nve all nve
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488 vel vfull method 1
thermo 200
run 5000
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000

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# GJF-2GJ thermostat
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
include ff-argon.lmp
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vhalf
fix nve all nve
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488
thermo 200
run 5000
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000

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LAMMPS (19 Sep 2019)
using 1 OpenMP thread(s) per MPI task
# GJF-2GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 1 by 1 MPI processor grid
reading atoms ...
864 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000150019 secs
read_data CPU = 0.001946 secs
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vfull
fix nve all nve
thermo 200
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.94072
ghost atom cutoff = 6.94072
binsize = 3.47036, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, 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) = 6.875 | 6.875 | 6.875 Mbytes
Step Temp E_pair E_mol TotEng Press
0 11.080223 -56.207655 0 -54.97164 37.215524
200 8.2588471 -55.073602 0 -54.152316 339.80416
400 8.1427292 -55.072244 0 -54.16391 338.91883
600 8.7595618 -55.066739 0 -54.089596 344.25426
800 8.550633 -55.148315 0 -54.194479 318.9385
1000 8.5394337 -55.125709 0 -54.173122 326.59471
1200 8.565973 -55.114892 0 -54.159345 328.5193
1400 8.2092914 -55.109233 0 -54.193475 329.56161
1600 8.209495 -55.138161 0 -54.22238 321.39971
1800 8.4039924 -55.13355 0 -54.196072 322.64214
2000 8.4548937 -55.062994 0 -54.119838 343.29888
2200 8.3775139 -55.13364 0 -54.199116 323.63744
2400 8.537332 -55.163702 0 -54.21135 315.62864
2600 8.672488 -55.112054 0 -54.144625 330.1106
2800 8.3000218 -55.147275 0 -54.221396 318.73112
3000 8.3552421 -55.135164 0 -54.203124 323.53075
3200 8.4126798 -55.135753 0 -54.197306 321.48817
3400 8.4986413 -55.135408 0 -54.187372 323.42951
3600 8.38431 -55.103932 0 -54.16865 330.68929
3800 8.8262454 -55.103648 0 -54.119067 332.97779
4000 7.9658136 -55.120402 0 -54.231803 324.9595
4200 8.2265544 -55.129011 0 -54.211327 323.87069
4400 8.1253738 -55.153089 0 -54.246691 316.304
4600 8.2010823 -55.124053 0 -54.20921 325.98402
4800 8.5512149 -55.075877 0 -54.121976 338.30137
5000 8.4737659 -55.158604 0 -54.213343 316.22418
Loop time of 2.73236 on 1 procs for 5000 steps with 864 atoms
Performance: 15810.507 ns/day, 0.002 hours/ns, 1829.920 timesteps/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 | 1.4262 | 1.4262 | 1.4262 | 0.0 | 52.20
Bond | 0.00042836 | 0.00042836 | 0.00042836 | 0.0 | 0.02
Neigh | 0.12819 | 0.12819 | 0.12819 | 0.0 | 4.69
Comm | 0.058611 | 0.058611 | 0.058611 | 0.0 | 2.15
Output | 0.00047283 | 0.00047283 | 0.00047283 | 0.0 | 0.02
Modify | 1.0924 | 1.0924 | 1.0924 | 0.0 | 39.98
Other | | 0.02605 | | | 0.95
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1593 ave 1593 max 1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18143 ave 18143 max 18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18143
Ave neighs/atom = 20.9988
Ave special neighs/atom = 0
Neighbor list builds = 158
Dangerous builds = 5
Total wall time: 0:00:02

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LAMMPS (19 Sep 2019)
using 1 OpenMP thread(s) per MPI task
# GJF-2GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 2 by 2 MPI processor grid
reading atoms ...
864 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000556268 secs
read_data CPU = 0.003817 secs
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vfull
fix nve all nve
thermo 200
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.94072
ghost atom cutoff = 6.94072
binsize = 3.47036, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, 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) = 6.808 | 6.808 | 6.808 Mbytes
Step Temp E_pair E_mol TotEng Press
0 11.080228 -56.207655 0 -54.971639 37.215541
200 8.4818184 -55.127334 0 -54.181174 324.96159
400 8.5960916 -55.09236 0 -54.133453 334.83136
600 8.1607556 -55.073136 0 -54.162791 339.035
800 8.8350489 -55.133382 0 -54.147819 324.48149
1000 8.5692704 -55.118463 0 -54.162548 327.26328
1200 8.4174147 -55.126297 0 -54.187322 324.4248
1400 8.6362603 -55.123075 0 -54.159688 326.7798
1600 8.222512 -55.153799 0 -54.236565 317.8147
1800 8.324523 -55.116698 0 -54.188085 327.35373
2000 7.9615959 -55.155825 0 -54.267697 315.37215
2200 8.495968 -55.083943 0 -54.136205 336.67775
2400 7.7926986 -55.044816 0 -54.175529 344.87758
2600 8.1551351 -55.069404 0 -54.159687 339.60901
2800 8.2593599 -55.084151 0 -54.162807 336.54935
3000 8.2860869 -55.110296 0 -54.185971 328.99074
3200 8.4074534 -55.123576 0 -54.185712 326.06823
3400 8.6694364 -55.128925 0 -54.161836 324.67512
3600 8.5718984 -55.129861 0 -54.173653 325.20586
3800 8.508102 -55.099093 0 -54.150001 333.91437
4000 8.2966658 -55.117782 0 -54.192276 327.13516
4200 8.7641728 -55.135792 0 -54.158136 324.00844
4400 8.8827909 -55.096369 0 -54.10548 335.08467
4600 8.7666577 -55.127213 0 -54.149279 326.15539
4800 8.6670762 -55.163395 0 -54.19657 316.48383
5000 8.1893094 -55.073756 0 -54.160226 337.95271
Loop time of 0.870594 on 4 procs for 5000 steps with 864 atoms
Performance: 49621.267 ns/day, 0.000 hours/ns, 5743.202 timesteps/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.33582 | 0.35125 | 0.3724 | 2.3 | 40.35
Bond | 0.00030267 | 0.00031316 | 0.00033538 | 0.0 | 0.04
Neigh | 0.034246 | 0.03479 | 0.035904 | 0.4 | 4.00
Comm | 0.15068 | 0.17419 | 0.19191 | 3.6 | 20.01
Output | 0.00044776 | 0.00054703 | 0.00083177 | 0.0 | 0.06
Modify | 0.27679 | 0.28079 | 0.28849 | 0.9 | 32.25
Other | | 0.02871 | | | 3.30
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 888.75 ave 899 max 876 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 4536 ave 4737 max 4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 178
Dangerous builds = 11
Total wall time: 0:00:00

125
examples/gjf/log.15Oct19.gjf.vhalf.g++.1
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@ -1,125 +0,0 @@
LAMMPS (19 Sep 2019)
using 1 OpenMP thread(s) per MPI task
# GJF-2GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 1 by 1 MPI processor grid
reading atoms ...
864 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000147804 secs
read_data CPU = 0.00194898 secs
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vhalf
fix nve all nve
thermo 200
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.94072
ghost atom cutoff = 6.94072
binsize = 3.47036, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, 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) = 6.5 | 6.5 | 6.5 Mbytes
Step Temp E_pair E_mol TotEng Press
0 11.080223 -56.207655 0 -54.97164 37.215524
200 9.8808568 -55.073602 0 -53.971378 345.62207
400 9.8712816 -55.072244 0 -53.971088 345.11889
600 10.528988 -55.066739 0 -53.892214 350.60093
800 10.167171 -55.148315 0 -54.014152 324.73679
1000 10.029026 -55.125709 0 -54.006956 331.93766
1200 10.194424 -55.114892 0 -53.977688 334.36032
1400 9.3473846 -55.109233 0 -54.066518 333.64378
1600 9.7774071 -55.138161 0 -54.047477 327.02358
1800 9.9814275 -55.13355 0 -54.020107 328.30017
2000 10.2515 -55.062994 0 -53.919424 349.74304
2200 9.8126922 -55.13364 0 -54.039019 328.78521
2400 10.044314 -55.163702 0 -54.043244 321.03397
2600 10.543316 -55.112054 0 -53.935932 336.82099
2800 9.7874375 -55.147275 0 -54.055472 324.06626
3000 9.7703821 -55.135164 0 -54.045263 328.60665
3200 10.141958 -55.135753 0 -54.004402 327.69084
3400 10.160576 -55.135408 0 -54.00198 329.39063
3600 10.044652 -55.103932 0 -53.983436 336.64469
3800 10.662403 -55.103648 0 -53.914241 339.56382
4000 9.2921047 -55.120402 0 -54.083853 329.71671
4200 9.8744553 -55.129011 0 -54.027501 329.78147
4400 9.4085964 -55.153089 0 -54.103546 320.90673
4600 9.5463801 -55.124053 0 -54.05914 330.80941
4800 10.223884 -55.075877 0 -53.935387 344.30099
5000 9.6243338 -55.158604 0 -54.084996 320.3511
Loop time of 2.29551 on 1 procs for 5000 steps with 864 atoms
Performance: 18819.358 ns/day, 0.001 hours/ns, 2178.166 timesteps/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 | 1.4393 | 1.4393 | 1.4393 | 0.0 | 62.70
Bond | 0.0004441 | 0.0004441 | 0.0004441 | 0.0 | 0.02
Neigh | 0.12136 | 0.12136 | 0.12136 | 0.0 | 5.29
Comm | 0.059342 | 0.059342 | 0.059342 | 0.0 | 2.59
Output | 0.00046968 | 0.00046968 | 0.00046968 | 0.0 | 0.02
Modify | 0.64937 | 0.64937 | 0.64937 | 0.0 | 28.29
Other | | 0.02522 | | | 1.10
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1593 ave 1593 max 1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18143 ave 18143 max 18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18143
Ave neighs/atom = 20.9988
Ave special neighs/atom = 0
Neighbor list builds = 158
Dangerous builds = 5
Total wall time: 0:00:02

125
examples/gjf/log.15Oct19.gjf.vhalf.g++.4
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@ -1,125 +0,0 @@
LAMMPS (19 Sep 2019)
using 1 OpenMP thread(s) per MPI task
# GJF-2GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 2 by 2 MPI processor grid
reading atoms ...
864 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000315903 secs
read_data CPU = 0.0653752 secs
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
fix lang all langevin 10 10 1 26488 gjf vhalf
fix nve all nve
thermo 200
run 5000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.94072
ghost atom cutoff = 6.94072
binsize = 3.47036, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, 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) = 6.433 | 6.433 | 6.433 Mbytes
Step Temp E_pair E_mol TotEng Press
0 11.080228 -56.207655 0 -54.971639 37.215541
200 9.8046716 -55.127334 0 -54.033608 329.70647
400 10.174622 -55.09236 0 -53.957366 340.49331
600 9.9812299 -55.073136 0 -53.959714 345.56477
800 10.512874 -55.133382 0 -53.960655 330.4996
1000 9.9587885 -55.118463 0 -54.007545 332.24728
1200 10.236607 -55.126297 0 -53.984388 330.94998
1400 10.134679 -55.123075 0 -53.992537 332.15441
1600 9.8934078 -55.153799 0 -54.050174 323.80795
1800 10.064966 -55.116698 0 -53.993936 333.59644
2000 9.6736107 -55.155825 0 -54.076719 321.5129
2200 10.264537 -55.083943 0 -53.938918 343.02135
2400 9.5640032 -55.044816 0 -53.977937 351.23099
2600 9.6581077 -55.069404 0 -53.992028 344.99996
2800 9.9622575 -55.084151 0 -53.972846 342.6574
3000 9.8724909 -55.110296 0 -54.009005 334.68094
3200 10.032027 -55.123576 0 -54.004488 331.89534
3400 10.221132 -55.128925 0 -53.988742 330.24082
3600 10.085802 -55.129861 0 -54.004774 330.63601
3800 10.098545 -55.099093 0 -53.972585 339.61905
4000 10.000257 -55.117782 0 -54.002238 333.24569
4200 10.20477 -55.135792 0 -53.997435 329.17565
4400 10.545132 -55.096369 0 -53.920044 341.04725
4600 10.376108 -55.127213 0 -53.969743 331.92825
4800 10.247392 -55.163395 0 -54.020283 322.15219
5000 9.7753102 -55.073756 0 -53.983305 343.64146
Loop time of 1.19785 on 4 procs for 5000 steps with 864 atoms
Performance: 36064.674 ns/day, 0.001 hours/ns, 4174.152 timesteps/s
88.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.36387 | 0.38652 | 0.44086 | 5.1 | 32.27
Bond | 0.00028847 | 0.00030833 | 0.000338 | 0.0 | 0.03
Neigh | 0.033934 | 0.034959 | 0.036917 | 0.6 | 2.92
Comm | 0.39292 | 0.47821 | 0.52198 | 7.3 | 39.92
Output | 0.00050343 | 0.0012343 | 0.0023338 | 1.9 | 0.10
Modify | 0.1605 | 0.17963 | 0.19457 | 2.9 | 15.00
Other | | 0.117 | | | 9.77
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 888.75 ave 899 max 876 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 4536 ave 4737 max 4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 178
Dangerous builds = 11
Total wall time: 0:00:01

193
examples/gjf/log.2Apr25.gjf.vfull.g++.1 Normal file
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@ -0,0 +1,193 @@
LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
Reading data file ...
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 1 by 1 MPI processor grid
reading atoms ...
864 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488 vel vfull method 1
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}
- GJ-I vfull method: doi:10.1080/00268976.2012.760055
@Article{gronbech-jensen_simple_2013,
title = {A simple and effective Verlet-type algorithm for simulating Langevin dynamics},
volume = {111},
url = {http://www.tandfonline.com/doi/abs/10.1080/00268976.2012.760055},
doi = {10.1080/00268976.2012.760055},
pages = {983-991},
number = {8},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels and Farago, Oded},
year = {2013}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9407173
ghost atom cutoff = 6.9407173
binsize = 3.4703587, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
5000 8.4535562 -55.150518 0 -54.207511 318.20862
Loop time of 2.26831 on 1 procs for 5000 steps with 864 atoms
Performance: 19044.977 ns/day, 0.001 hours/ns, 2204.280 timesteps/s, 1.904 Matom-step/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 | 1.2802 | 1.2802 | 1.2802 | 0.0 | 56.44
Bond | 0.00051213 | 0.00051213 | 0.00051213 | 0.0 | 0.02
Neigh | 0.27007 | 0.27007 | 0.27007 | 0.0 | 11.91
Comm | 0.057527 | 0.057527 | 0.057527 | 0.0 | 2.54
Output | 6.3876e-05 | 6.3876e-05 | 6.3876e-05 | 0.0 | 0.00
Modify | 0.63364 | 0.63364 | 0.63364 | 0.0 | 27.93
Other | | 0.02635 | | | 1.16
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1593 ave 1593 max 1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18143 ave 18143 max 18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 258
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 8.4535562 -55.150518 0 -54.207511 318.20862
6000 8.4899401 -55.108242 0 -54.161176 331.10703
8000 8.3618893 -55.092171 0 -54.15939 334.11831
10000 8.8684311 -55.100316 0 -54.111029 334.09931
12000 8.4339192 -55.07343 0 -54.132614 340.00487
14000 8.072393 -55.115121 0 -54.214633 327.98965
16000 8.3420289 -55.077813 0 -54.147247 337.74926
18000 8.3803911 -55.12201 0 -54.187164 326.10485
20000 8.4676985 -55.176339 0 -54.231754 311.57092
22000 8.8560138 -55.110505 0 -54.122603 330.66179
24000 8.3187826 -55.120592 0 -54.192619 327.01148
26000 8.0327666 -55.116664 0 -54.220596 326.25179
28000 8.3672169 -55.130413 0 -54.197037 324.2368
30000 8.1669275 -55.057678 0 -54.146645 344.9168
32000 8.3819314 -55.08989 0 -54.154873 335.45317
34000 8.109088 -55.17222 0 -54.267639 310.83717
36000 8.3048574 -55.079475 0 -54.153056 338.04291
38000 8.8708544 -55.108991 0 -54.119434 330.70097
40000 8.4012779 -55.080817 0 -54.143642 338.54326
Loop time of 18.9699 on 1 procs for 35000 steps with 864 atoms
Performance: 15941.040 ns/day, 0.002 hours/ns, 1845.028 timesteps/s, 1.594 Matom-step/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 | 11.593 | 11.593 | 11.593 | 0.0 | 61.11
Bond | 0.0041801 | 0.0041801 | 0.0041801 | 0.0 | 0.02
Neigh | 2.2671 | 2.2671 | 2.2671 | 0.0 | 11.95
Comm | 0.42339 | 0.42339 | 0.42339 | 0.0 | 2.23
Output | 0.00062204 | 0.00062204 | 0.00062204 | 0.0 | 0.00
Modify | 4.4976 | 4.4976 | 4.4976 | 0.0 | 23.71
Other | | 0.1839 | | | 0.97
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1592 ave 1592 max 1592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18144 ave 18144 max 18144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 2122
Dangerous builds = 0
Total wall time: 0:00:21

193
examples/gjf/log.2Apr25.gjf.vfull.g++.4 Normal file
View File

@ -0,0 +1,193 @@
LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
Reading data file ...
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 2 by 2 MPI processor grid
reading atoms ...
864 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.015 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488 vel vfull method 1
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}
- GJ-I vfull method: doi:10.1080/00268976.2012.760055
@Article{gronbech-jensen_simple_2013,
title = {A simple and effective Verlet-type algorithm for simulating Langevin dynamics},
volume = {111},
url = {http://www.tandfonline.com/doi/abs/10.1080/00268976.2012.760055},
doi = {10.1080/00268976.2012.760055},
pages = {983-991},
number = {8},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels and Farago, Oded},
year = {2013}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9407173
ghost atom cutoff = 6.9407173
binsize = 3.4703587, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.427 | 6.427 | 6.427 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
5000 7.946377 -55.076514 0 -54.190084 337.31999
Loop time of 2.0998 on 4 procs for 5000 steps with 864 atoms
Performance: 20573.405 ns/day, 0.001 hours/ns, 2381.181 timesteps/s, 2.057 Matom-step/s
65.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53641 | 0.54389 | 0.54721 | 0.6 | 25.90
Bond | 0.00056487 | 0.0006195 | 0.00068462 | 0.0 | 0.03
Neigh | 0.10567 | 0.1086 | 0.11128 | 0.7 | 5.17
Comm | 0.96913 | 0.97758 | 0.98191 | 0.5 | 46.56
Output | 0.00025213 | 0.00025642 | 0.00026405 | 0.0 | 0.01
Modify | 0.25061 | 0.25105 | 0.25172 | 0.1 | 11.96
Other | | 0.2178 | | | 10.37
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 884.75 ave 885 max 884 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 4536 ave 4737 max 4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 273
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.428 | 6.428 | 6.428 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 7.946377 -55.076514 0 -54.190084 337.31999
6000 8.2565866 -55.129244 0 -54.208209 324.57967
8000 7.9942397 -55.101417 0 -54.209648 331.24127
10000 8.5413968 -55.083292 0 -54.130486 337.82599
12000 8.3682078 -55.090905 0 -54.157419 335.08066
14000 8.5082065 -55.085051 0 -54.135948 336.2765
16000 8.1944037 -55.090733 0 -54.176635 334.03786
18000 8.2607106 -55.030131 0 -54.108637 352.49892
20000 8.1154691 -55.104072 0 -54.198779 330.14203
22000 8.5592601 -55.152019 0 -54.197221 318.03507
24000 8.3182914 -55.115242 0 -54.187324 328.46084
26000 8.3691375 -55.125275 0 -54.191685 325.43673
28000 8.531632 -55.107097 0 -54.155381 331.42771
30000 8.1102222 -55.099011 0 -54.194304 332.04678
32000 8.5558571 -55.077016 0 -54.122598 339.87746
34000 8.4213946 -55.097068 0 -54.157649 333.34935
36000 8.0936615 -55.152202 0 -54.249342 316.20169
38000 7.999652 -55.048407 0 -54.156034 345.07945
40000 8.6699753 -55.087634 0 -54.120485 337.23709
Loop time of 17.6726 on 4 procs for 35000 steps with 864 atoms
Performance: 17111.263 ns/day, 0.001 hours/ns, 1980.470 timesteps/s, 1.711 Matom-step/s
65.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0739 | 5.1178 | 5.1689 | 1.5 | 28.96
Bond | 0.0043764 | 0.004688 | 0.0051706 | 0.4 | 0.03
Neigh | 0.83797 | 0.85506 | 0.87554 | 1.8 | 4.84
Comm | 6.816 | 6.8932 | 6.9215 | 1.7 | 39.00
Output | 0.0043624 | 0.0045336 | 0.004998 | 0.4 | 0.03
Modify | 3.3008 | 3.3033 | 3.3066 | 0.1 | 18.69
Other | | 1.494 | | | 8.45
Nlocal: 216 ave 222 max 210 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 905.5 ave 911 max 899 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 4535.75 ave 4837 max 4218 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 2140
Dangerous builds = 0
Total wall time: 0:00:19

192
examples/gjf/log.2Apr25.gjf.vhalf.g++.1 Normal file
View File

@ -0,0 +1,192 @@
LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
Reading data file ...
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 1 by 1 MPI processor grid
reading atoms ...
864 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.010 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}
- GJ-I vhalf method: doi:10.1080/00268976.2019.1570369
@Article{jensen_accurate_2019,
title = {Accurate configurational and kinetic statistics in discrete-time Langevin systems},
volume = {117},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1570369},
doi = {10.1080/00268976.2019.1570369},
number = {18},
journal = {Molecular Physics},
author = {Jensen, Lucas Frese Grønbech and Grønbech-Jensen, Niels},
year = {2019}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9407173
ghost atom cutoff = 6.9407173
binsize = 3.4703587, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
5000 9.7731898 -55.150518 0 -54.060304 322.94195
Loop time of 2.28421 on 1 procs for 5000 steps with 864 atoms
Performance: 18912.438 ns/day, 0.001 hours/ns, 2188.940 timesteps/s, 1.891 Matom-step/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 | 1.2715 | 1.2715 | 1.2715 | 0.0 | 55.66
Bond | 0.00057126 | 0.00057126 | 0.00057126 | 0.0 | 0.03
Neigh | 0.27008 | 0.27008 | 0.27008 | 0.0 | 11.82
Comm | 0.057938 | 0.057938 | 0.057938 | 0.0 | 2.54
Output | 6.1954e-05 | 6.1954e-05 | 6.1954e-05 | 0.0 | 0.00
Modify | 0.658 | 0.658 | 0.658 | 0.0 | 28.81
Other | | 0.0261 | | | 1.14
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1593 ave 1593 max 1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18143 ave 18143 max 18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 258
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 9.7731898 -55.150518 0 -54.060304 322.94195
6000 10.024842 -55.108242 0 -53.989956 336.6125
8000 10.118994 -55.092171 0 -53.963382 340.42078
10000 10.541359 -55.100316 0 -53.924412 340.09986
12000 10.023234 -55.07343 0 -53.955323 345.70551
14000 9.5912018 -55.115121 0 -54.045208 333.43739
16000 9.9450498 -55.077813 0 -53.968428 343.49906
18000 10.113744 -55.12201 0 -53.993806 332.32214
20000 9.9345204 -55.176339 0 -54.068128 316.83219
22000 10.585719 -55.110505 0 -53.929652 336.86599
24000 10.024757 -55.120592 0 -54.002315 333.13056
26000 9.7787474 -55.116664 0 -54.02583 332.51437
28000 9.6092087 -55.130413 0 -54.058491 328.69165
30000 9.8245787 -55.057678 0 -53.961731 350.86255
32000 10.066994 -55.08989 0 -53.966902 341.49724
34000 9.5677059 -55.17222 0 -54.104928 316.06902
36000 9.7252627 -55.079475 0 -53.994608 343.13769
38000 10.438984 -55.108991 0 -53.944506 336.32562
40000 10.238268 -55.080817 0 -53.938723 345.13228
Loop time of 19.138 on 1 procs for 35000 steps with 864 atoms
Performance: 15801.041 ns/day, 0.002 hours/ns, 1828.824 timesteps/s, 1.580 Matom-step/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 | 11.568 | 11.568 | 11.568 | 0.0 | 60.44
Bond | 0.0042372 | 0.0042372 | 0.0042372 | 0.0 | 0.02
Neigh | 2.2577 | 2.2577 | 2.2577 | 0.0 | 11.80
Comm | 0.42841 | 0.42841 | 0.42841 | 0.0 | 2.24
Output | 0.00060128 | 0.00060128 | 0.00060128 | 0.0 | 0.00
Modify | 4.694 | 4.694 | 4.694 | 0.0 | 24.53
Other | | 0.1852 | | | 0.97
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1592 ave 1592 max 1592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18144 ave 18144 max 18144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 2122
Dangerous builds = 0
Total wall time: 0:00:21

192
examples/gjf/log.2Apr25.gjf.vhalf.g++.4 Normal file
View File

@ -0,0 +1,192 @@
LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# GJ thermostat
units metal
atom_style full
boundary p p p
read_data argon.lmp
Reading data file ...
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
1 by 2 by 2 MPI processor grid
reading atoms ...
864 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.015 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
variable Ar equal 1
#############
#Atom Masses#
#############
mass ${Ar} 39.903
mass 1 39.903
###########################
#Pair Potentials - Tersoff#
###########################
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin
timestep 0.1
compute myKE all ke
compute myPE all pe
fix lang all gjf 10 10 1 26488
run 5000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GJ methods: doi:10.1080/00268976.2019.1662506
@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}
- GJ-I vhalf method: doi:10.1080/00268976.2019.1570369
@Article{jensen_accurate_2019,
title = {Accurate configurational and kinetic statistics in discrete-time Langevin systems},
volume = {117},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1570369},
doi = {10.1080/00268976.2019.1570369},
number = {18},
journal = {Molecular Physics},
author = {Jensen, Lucas Frese Grønbech and Grønbech-Jensen, Niels},
year = {2019}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.9407173
ghost atom cutoff = 6.9407173
binsize = 3.4703587, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.427 | 6.427 | 6.427 Mbytes
Step Temp E_pair E_mol TotEng Press
0 10 -56.207652 0 -55.092137 33.341103
5000 9.3726166 -55.076514 0 -54.030985 342.43571
Loop time of 2.11818 on 4 procs for 5000 steps with 864 atoms
Performance: 20394.822 ns/day, 0.001 hours/ns, 2360.512 timesteps/s, 2.039 Matom-step/s
63.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53987 | 0.54922 | 0.56044 | 1.2 | 25.93
Bond | 0.00058281 | 0.00063674 | 0.00075153 | 0.0 | 0.03
Neigh | 0.10821 | 0.10912 | 0.11017 | 0.2 | 5.15
Comm | 0.96075 | 0.97484 | 0.98645 | 1.1 | 46.02
Output | 0.00026318 | 0.00026575 | 0.00027192 | 0.0 | 0.01
Modify | 0.26142 | 0.2634 | 0.26465 | 0.2 | 12.44
Other | | 0.2207 | | | 10.42
Nlocal: 216 ave 216 max 216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 884.75 ave 885 max 884 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 4536 ave 4737 max 4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 273
Dangerous builds = 0
fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out
thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.428 | 6.428 | 6.428 Mbytes
Step Temp E_pair E_mol TotEng Press
5000 9.3726166 -55.076514 0 -54.030985 342.43571
6000 9.6911866 -55.129244 0 -54.048177 329.72537
8000 9.7296551 -55.101417 0 -54.016059 337.46595
10000 10.098808 -55.083292 0 -53.956755 343.4122
12000 10.114344 -55.090905 0 -53.962635 341.3438
14000 10.230012 -55.085051 0 -53.943878 342.45237
16000 9.5989709 -55.090733 0 -54.019954 339.07584
18000 10.016071 -55.030131 0 -53.912824 358.79514
20000 9.7197057 -55.104072 0 -54.019824 335.89619
22000 9.959647 -55.152019 0 -54.041005 323.05805
24000 10.075138 -55.115242 0 -53.991345 334.76239
26000 10.227192 -55.125275 0 -53.984416 332.10131
28000 10.177109 -55.107097 0 -53.971825 337.32979
30000 9.521036 -55.099011 0 -54.036925 337.10716
32000 10.265633 -55.077016 0 -53.93187 346.01018
34000 10.173978 -55.097068 0 -53.962146 339.63562
36000 9.6032778 -55.152202 0 -54.080942 321.61646
38000 9.8802995 -55.048407 0 -53.946245 351.82506
40000 10.372288 -55.087634 0 -53.93059 343.34304
Loop time of 17.867 on 4 procs for 35000 steps with 864 atoms
Performance: 16925.013 ns/day, 0.001 hours/ns, 1958.914 timesteps/s, 1.693 Matom-step/s
65.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0932 | 5.1683 | 5.2256 | 2.5 | 28.93
Bond | 0.0044473 | 0.0048347 | 0.0058137 | 0.8 | 0.03
Neigh | 0.85262 | 0.8601 | 0.87438 | 0.9 | 4.81
Comm | 6.8164 | 6.8981 | 6.9859 | 2.6 | 38.61
Output | 0.0046884 | 0.0047093 | 0.0047322 | 0.0 | 0.03
Modify | 3.4107 | 3.4186 | 3.4248 | 0.3 | 19.13
Other | | 1.512 | | | 8.47
Nlocal: 216 ave 222 max 210 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 905.5 ave 911 max 899 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 4535.75 ave 4837 max 4218 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 2140
Dangerous builds = 0
Total wall time: 0:00:21

18
examples/granular/data.particles
View File

@ -1,18 +0,0 @@
Python generated LAMMPS data file
2 atoms
1 atom types
0 0.08 xlo xhi
0 0.04 ylo yhi
0 0.08 zlo zhi
Atoms # sphere
1 1 0.004 2500 0.04 0.02 0.04 0 0 0
2 1 0.004 2500 0.04 0.02 0.04416 0 0 0
Velocities
1 0.0 0.0 1 0 0 0
2 0.0 0.0 -1 0 0 0

47
examples/granular/in.restitution
View File

@ -1,24 +1,43 @@
units si
atom_style sphere
comm_modify vel yes
boundary p p p
boundary p p f
region box block 0 80e-3 0 40e-3 0 80e-3 open 3 open 4
region box block -0.01 0.01 -0.01 0.01 0 0.08
create_box 2 box
read_data data.particles add append
group mb type 1
create_atoms 1 single 0.0 0.0 0.04
create_atoms 1 single 0.0 0.0 0.04416
set group all diameter 0.004 density 2500
pair_style granular
pair_coeff * * hertz/material 1e6 0.8 0.4 tangential mindlin NULL 0.0 0.5 damping coeff_restitution
# pair_coeff * * hooke 1e6 0.5 tangential mindlin 1 1.0 0.0 damping coeff_restitution
comm_modify vel yes
pair_style granular
pair_coeff * * hertz/material 1e6 0.8 0.4 &
tangential mindlin NULL 0.0 0.5 &
damping coeff_restitution
#pair_coeff * * hooke 1e6 0.5 &
# tangential mindlin 1 1.0 0.0 &
# damping coeff_restitution
timestep 1e-9
fix 1 all nve/sphere
compute s all stress/atom NULL pair
#dump 1 all custom 2000000 op.dump id x y z vx vy vz
#dump_modify 1 pad 8
thermo_style custom step ke
run_style verlet
run 10000000
group a1 id 1
group a2 id 2
velocity a1 set 0 0 1.0
velocity a2 set 0 0 -1.0
compute z1 a1 reduce sum z
compute z2 a2 reduce sum z
compute v1 a1 reduce sum vz
compute v2 a2 reduce sum vz
compute f1 a1 reduce sum fz
compute f2 a2 reduce sum fz
variable dz equal c_z1 - c_z2
# dump 1 all custom 2000000 op.dump id x y z vx vy vz
thermo 10000
thermo_style custom step ke v_dz c_v1 c_v2 c_f1 c_f2
run 1000000

24
examples/granular/in.tableting.200
View File

@ -28,19 +28,20 @@ variable dieHeight equal 1e-2
pair_style granular
# mdr = E, nu, Y, gamma, psi_b, CoR
# mdr = E, nu, Y, gamma, psi_b, damp
variable YoungsModulus equal 5e6
variable YieldStress equal 1.9e5
variable PoissonsRatio equal 0.4
variable SurfaceEnergy equal 2
variable SurfaceEnergyWall equal 0.0
variable CoR equal 0.5
variable psi_b equal 0.5
variable damp equal 0.2
variable damp_type equal 1
# linear_history = k_t, x_gammat, mu_s
variable kt equal 2/7*${YoungsModulus}*${atomRadius}
variable kt_wall equal 2/7*${YoungsModulus}*${atomRadius}
variable xgammat equal 0.0
variable xgammat equal 1.0
variable mu_s equal 0.7
variable mu_s_wall equal 0.1
@ -49,14 +50,17 @@ variable mu_roll equal 0.6
variable k_roll equal 2.25*${mu_roll}*${mu_roll}*${YoungsModulus}*${atomRadius}
variable gamma_roll equal 0.0
pair_coeff * * mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${CoR} tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll} damping none
pair_coeff * * mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} &
damping mdr ${damp_type} &
tangential linear_history ${kt} ${xgammat} ${mu_s} &
rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
######################################### ADD DIE AND PUNCH WALLS ############################################
variable disp_upper equal 0.0
variable disp_lower equal 0.0
variable wall_contact_string string "granular mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergyWall} ${psi_b} ${CoR} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll} damping none"
variable wall_contact_string string "granular mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergyWall} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}"
variable dieHeight2 equal 2*${dieHeight}
@ -73,7 +77,7 @@ variable avgUpperPunchForce equal c_avgUpperPunchForce
compute avgLowerPunchForce all reduce sum f_lowerPunch[4]
variable avgLowerPunchForce equal c_avgLowerPunchForce
fix printFD all print 1 "${disp_upper} ${avgUpperPunchForce} ${avgLowerPunchForce}" file punch_force_disp_tableting200.csv screen no
#fix printFD all print 1 "${disp_upper} ${avgUpperPunchForce} ${avgLowerPunchForce}" file punch_force_disp_tableting200.csv screen no
##################################### INTEGRATION AND GRAVITY #################################################
@ -109,13 +113,13 @@ variable syy_ave equal c_sigmayy_ave
variable szz_ave equal c_sigmazz_ave
variable Vparticles equal c_Velas_sum
fix log all print 1 "${sxx_ave} ${syy_ave} ${szz_ave} ${Vparticles}" file average_normal_stresses_tableting200.csv screen no
dump dumpParticles all custom ${output_rate} tableting200.dump id type mass diameter x y z vx vy vz fx fy fz c_ke c_sigmaxx c_sigmayy c_sigmazz
#fix log all print 1 "${sxx_ave} ${syy_ave} ${szz_ave} ${Vparticles}" file average_normal_stresses_tableting200.csv screen no
#dump dumpParticles all custom ${output_rate} tableting200.dump id type mass diameter x y z vx vy vz fx fy fz c_ke c_sigmaxx c_sigmayy c_sigmazz
#dump dumpParticlesVTK all vtk ${output_rate} post/particles_*.vtk id x y z fx fy fz vx vy vz c_ke radius c_sigmaxx c_sigmayy c_sigmazz
############################################## RUN SIMULATION #################################################
variable upper_punch_stroke equal 0.6733*${dieHeight}
variable upper_punch_stroke equal 0.7*${dieHeight}
variable vel_upper equal 0.25
variable settling_steps equal round(0.02/dt)
@ -146,4 +150,4 @@ run ${ejection_steps}
variable disp_lower equal ${dieHeight}
variable disp_upper equal ${dieHeight}*0.9
variable max_disp equal ${dieRadius}*0.75
run ${free_float_steps}
run ${free_float_steps}

25
examples/granular/in.triaxial.compaction.12
View File

@ -1,7 +1,7 @@
############################### SIMULATION SETTINGS ###################################################
atom_style sphere 1
atom_modify map array
atom_modify map array
comm_modify vel yes
units si
newton off
@ -24,20 +24,23 @@ variable atomRadius equal 0.5
pair_style granular
# mdr = E, nu, Y, gamma, psi_b, CoR
# mdr = E, nu, Y, gamma, psi_b, damp
variable YoungsModulus equal 1e9
variable PoissonsRatio equal 0.3
variable YieldStress equal 50e6
variable SurfaceEnergy equal 0.0
variable psi_b equal 0.5
variable CoR equal 0.5
variable damp equal 0.2
variable damp_type equal 1
# linear_history = k_t, x_gamma,t, mu_s
variable kt equal 2/7*${YoungsModulus}*${atomRadius}
variable xgammat equal 0.0
variable mu_s equal 0.5
pair_coeff * * mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${CoR} tangential linear_history ${kt} ${xgammat} ${mu_s} damping none
pair_coeff * * mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} &
damping mdr ${damp_type} &
tangential linear_history ${kt} ${xgammat} ${mu_s}
######################################### ADD IN PLANES ################################################
@ -54,7 +57,7 @@ region plane_xz_neg plane 0 -${halfBoxWidth} 0 0 1 0 side in move NULL v_plane_d
region plane_xy_pos plane 0 0 ${halfBoxWidth} 0 0 -1 side in move NULL NULL v_plane_disp_neg units box
region plane_xy_neg plane 0 0 -${halfBoxWidth} 0 0 1 side in move NULL NULL v_plane_disp units box
variable wall_contact_string string "granular mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${CoR} tangential linear_history ${kt} ${xgammat} ${mu_s} damping none"
variable wall_contact_string string "granular mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s} "
fix plane_yz_pos all wall/gran/region ${wall_contact_string} region plane_yz_pos contacts
fix plane_yz_neg all wall/gran/region ${wall_contact_string} region plane_yz_neg contacts
@ -72,12 +75,12 @@ variable plane_xz_neg_force equal c_plane_xz_neg_force
compute plane_yz_neg_force all reduce sum f_plane_yz_neg[2]
variable plane_yz_neg_force equal c_plane_yz_neg_force
fix print1 all print 1 "${plane_disp} ${plane_xy_neg_force} ${plane_xz_neg_force} ${plane_yz_neg_force}" file force_disp_triaxial12.csv screen no
#fix print1 all print 1 "${plane_disp} ${plane_xy_neg_force} ${plane_xz_neg_force} ${plane_yz_neg_force}" file force_disp_triaxial12.csv screen no
######################################## SCREEN OUTPUT ####################################################
######################################## SCREEN OUTPUT ####################################################
compute 1 all erotate/sphere
thermo_style custom dt step atoms ke c_1 vol
thermo_style custom dt step atoms ke c_1 vol
thermo 100
thermo_modify lost ignore norm no
@ -89,8 +92,8 @@ variable compression_steps equal round(${disp_max}/${ddisp})
variable output_rate equal round(${compression_steps}/100)
##################################### SET UP DUMP OUTPUTS ####################################################
dump dumpParticles all custom ${output_rate} triaxial_compaction_12.dump id type mass x y z vx vy vz fx fy fz radius
#dump dumpParticles all custom ${output_rate} triaxial_compaction_12.dump id type mass x y z vx vy vz fx fy fz radius
#dump dmp all vtk ${output_rate} post/triaxial12particles_*.vtk id type mass x y z vx vy vz fx fy fz radius
#################################### COMPRESS THE PARTICLES ##################################################
@ -101,7 +104,7 @@ run 0
compute Ac_1_12 particles_1_12 pair/local p13 cutoff radius
compute Ac_1_12_sum particles_1_12 reduce sum c_Ac_1_12 inputs local
variable Ac_1_12 equal c_Ac_1_12_sum
fix logArea all print 100 "${plane_disp} ${Ac_1_12}" file pair_1_12_contact_area_triaxial12.csv screen no
#fix logArea all print 100 "${plane_disp} ${Ac_1_12}" file pair_1_12_contact_area_triaxial12.csv screen no
variable plane_disp equal ${ddisp}*elapsed
variable plane_disp_neg equal -${ddisp}*elapsed

80
examples/granular/log.13May23.restitution.g++.1
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@ -1,80 +0,0 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-93-g4e7bddaa0b)
using 1 OpenMP thread(s) per MPI task
units si
atom_style sphere
boundary p p f
region box block 0 80e-3 0 40e-3 0 80e-3 open 3 open 4
create_box 2 box
Created orthogonal box = (0 0 0) to (0.08 0.04 0.08)
1 by 1 by 1 MPI processor grid
read_data data.particles add append
Reading data file ...
orthogonal box = (0 0 0) to (0.08 0.04 0.08)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
reading velocities ...
2 velocities
read_data CPU = 0.002 seconds
group mb type 1
2 atoms in group mb
pair_style granular
pair_coeff * * hertz/material 1e6 0.8 0.4 tangential mindlin NULL 0.0 0.5 damping coeff_restitution
# pair_coeff * * hooke 1e6 0.5 tangential mindlin 1 1.0 0.0 damping coeff_restitution
comm_modify vel yes
timestep 1e-9
fix 1 all nve/sphere
compute s all stress/atom NULL pair
#dump 1 all custom 2000000 op.dump id x y z vx vy vz
#dump_modify 1 pad 8
thermo_style custom step ke
run_style verlet
run 10000000
Generated 0 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 = 0.005
ghost atom cutoff = 0.005
binsize = 0.0025, bins = 32 16 32
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.1 | 10.1 | 10.1 Mbytes
Step KinEng
0 8.3775804e-05
10000000 5.3616513e-05
Loop time of 5.99782 on 1 procs for 10000000 steps with 2 atoms
77.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.60235 | 0.60235 | 0.60235 | 0.0 | 10.04
Neigh | 0.00021965 | 0.00021965 | 0.00021965 | 0.0 | 0.00
Comm | 1.7939 | 1.7939 | 1.7939 | 0.0 | 29.91
Output | 2.5955e-05 | 2.5955e-05 | 2.5955e-05 | 0.0 | 0.00
Modify | 1.7622 | 1.7622 | 1.7622 | 0.0 | 29.38
Other | | 1.839 | | | 30.66
Nlocal: 2 ave 2 max 2 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: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 14
Dangerous builds = 0
Total wall time: 0:00:06

195
examples/granular/log.4Feb25.restitution.g++.1 Normal file
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@ -0,0 +1,195 @@
LAMMPS (4 Feb 2025)
units si
atom_style sphere
comm_modify vel yes
boundary p p p
region box block -0.01 0.01 -0.01 0.01 0 0.08
create_box 2 box
Created orthogonal box = (-0.01 -0.01 0) to (0.01 0.01 0.08)
1 by 1 by 1 MPI processor grid
create_atoms 1 single 0.0 0.0 0.04
Created 1 atoms
using lattice units in orthogonal box = (-0.01 -0.01 0) to (0.01 0.01 0.08)
create_atoms CPU = 0.000 seconds
create_atoms 1 single 0.0 0.0 0.04416
Created 1 atoms
using lattice units in orthogonal box = (-0.01 -0.01 0) to (0.01 0.01 0.08)
create_atoms CPU = 0.000 seconds
set group all diameter 0.004 density 2500
Setting atom values ...
2 settings made for diameter
2 settings made for density
pair_style granular
pair_coeff * * hertz/material 1e6 0.8 0.4 tangential mindlin NULL 0.0 0.5 damping coeff_restitution
#pair_coeff * * hooke 1e6 0.5 # tangential mindlin 1 1.0 0.0 # damping coeff_restitution
timestep 1e-9
fix 1 all nve/sphere
group a1 id 1
1 atoms in group a1
group a2 id 2
1 atoms in group a2
velocity a1 set 0 0 1.0
velocity a2 set 0 0 -1.0
compute z1 a1 reduce sum z
compute z2 a2 reduce sum z
compute v1 a1 reduce sum vz
compute v2 a2 reduce sum vz
compute f1 a1 reduce sum fz
compute f2 a2 reduce sum fz
variable dz equal c_z1 - c_z2
# dump 1 all custom 2000000 op.dump id x y z vx vy vz
thermo 10000
thermo_style custom step ke v_dz c_v1 c_v2 c_f1 c_f2
run 1000000
Generated 0 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 = 0.005
ghost atom cutoff = 0.005
binsize = 0.0025, bins = 8 8 32
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.998 | 9.998 | 9.998 Mbytes
Step KinEng v_dz c_v1 c_v2 c_f1 c_f2
0 8.3775804e-05 -0.00416 1 -1 0 0
10000 8.3775804e-05 -0.00414 1 -1 0 0
20000 8.3775804e-05 -0.00412 1 -1 0 0
30000 8.3775804e-05 -0.0041 1 -1 0 0
40000 8.3775804e-05 -0.00408 1 -1 0 0
50000 8.3775804e-05 -0.00406 1 -1 0 0
60000 8.3775804e-05 -0.00404 1 -1 0 0
70000 8.3775804e-05 -0.00402 1 -1 0 0
80000 8.3775804e-05 -0.004 1 -1 0 0
90000 8.3411065e-05 -0.003980019 0.99782075 -0.99782075 -0.023914747 0.023914747
100000 8.2852688e-05 -0.0039600945 0.9944753 -0.9944753 -0.032005131 0.032005131
110000 8.2139641e-05 -0.0039402463 0.99018672 -0.99018672 -0.039875404 0.039875404
120000 8.1272296e-05 -0.0039204934 0.98494496 -0.98494496 -0.048007824 0.048007824
130000 8.0246788e-05 -0.0039008551 0.97871113 -0.97871113 -0.056503872 0.056503872
140000 7.9058986e-05 -0.0038813518 0.97144075 -0.97144075 -0.065373554 0.065373554
150000 7.7705654e-05 -0.0038620047 0.9630903 -0.9630903 -0.074595879 0.074595879
160000 7.6184906e-05 -0.0038428357 0.95361959 -0.95361959 -0.084137355 0.084137355
170000 7.4496418e-05 -0.0038238676 0.94299284 -0.94299284 -0.093958893 0.093958893
180000 7.2641536e-05 -0.0038051239 0.93117907 -0.93117907 -0.10401872 0.10401872
190000 7.0623328e-05 -0.0037866285 0.91815243 -0.91815243 -0.11427372 0.11427372
200000 6.8446602e-05 -0.003768406 0.90389221 -0.90389221 -0.12468011 0.12468011
210000 6.6117901e-05 -0.0037504812 0.88838298 -0.88838298 -0.13519381 0.13519381
220000 6.3645478e-05 -0.0037328791 0.87161455 -0.87161455 -0.14577066 0.14577066
230000 6.1039243e-05 -0.003715625 0.85358204 -0.85358204 -0.1563666 0.1563666
240000 5.8310702e-05 -0.0036987442 0.83428576 -0.83428576 -0.16693776 0.16693776
250000 5.5472871e-05 -0.003682262 0.8137313 -0.8137313 -0.17744066 0.17744066
260000 5.2540172e-05 -0.0036662033 0.79192936 -0.79192936 -0.18783225 0.18783225
270000 4.9528314e-05 -0.003650593 0.76889577 -0.76889577 -0.19807012 0.19807012
280000 4.6454158e-05 -0.0036354555 0.74465137 -0.74465137 -0.20811258 0.20811258
290000 4.3335566e-05 -0.0036208149 0.71922195 -0.71922195 -0.21791884 0.21791884
300000 4.0191232e-05 -0.0036066944 0.69263807 -0.69263807 -0.22744912 0.22744912
310000 3.7040511e-05 -0.0035931168 0.66493499 -0.66493499 -0.23666485 0.23666485
320000 3.390323e-05 -0.0035801042 0.63615249 -0.63615249 -0.24552878 0.24552878
330000 3.0799488e-05 -0.0035676776 0.60633473 -0.60633473 -0.25400513 0.25400513
340000 2.7749462e-05 -0.0035558573 0.57553002 -0.57553002 -0.26205979 0.26205979
350000 2.4773197e-05 -0.0035446626 0.54379063 -0.54379063 -0.2696604 0.2696604
360000 2.1890403e-05 -0.0035341116 0.51117262 -0.51117262 -0.27677654 0.27677654
370000 1.9120254e-05 -0.0035242212 0.47773551 -0.47773551 -0.28337983 0.28337983
380000 1.6481181e-05 -0.0035150072 0.44354212 -0.44354212 -0.28944409 0.28944409
390000 1.3990689e-05 -0.0035064841 0.40865822 -0.40865822 -0.29494544 0.29494544
400000 1.1665166e-05 -0.003498665 0.37315233 -0.37315233 -0.2998624 0.2998624
410000 9.5197195e-06 -0.0034915617 0.33709536 -0.33709536 -0.304176 0.304176
420000 7.5680136e-06 -0.0034851844 0.30056032 -0.30056032 -0.30786987 0.30786987
430000 5.8221324e-06 -0.003479542 0.26362205 -0.26362205 -0.31093026 0.31093026
440000 4.2924559e-06 -0.0034746417 0.22635684 -0.22635684 -0.31334618 0.31334618
450000 2.9875585e-06 -0.0034704894 0.18884214 -0.18884214 -0.31510936 0.31510936
460000 1.9141264e-06 -0.0034670891 0.15115621 -0.15115621 -0.31621432 0.31621432
470000 1.0768988e-06 -0.0034644437 0.11337783 -0.11337783 -0.31665837 0.31665837
480000 4.786302e-07 -0.0034625541 0.075585893 -0.075585893 -0.31644161 0.31644161
490000 1.2007709e-07 -0.0034614198 0.037859142 -0.037859142 -0.31556689 0.31556689
500000 6.3727744e-12 -0.0034610388 0.0002758068 -0.0002758068 -0.31403982 0.31403982
510000 1.1522726e-07 -0.0034614073 -0.03708671 0.03708671 -0.31186864 0.31186864
520000 4.6064472e-07 -0.0034625203 -0.074152149 0.074152149 -0.30906426 0.30906426
530000 1.029334e-06 -0.0034643709 -0.1108457 0.1108457 -0.30564009 0.30564009
540000 1.812635e-06 -0.0034669512 -0.14709431 0.14709431 -0.30161199 0.30161199
550000 2.8002645e-06 -0.0034702513 -0.18282695 0.18282695 -0.29699817 0.29699817
560000 3.9804448e-06 -0.0034742603 -0.21797491 0.21797491 -0.29181905 0.29181905
570000 5.3400475e-06 -0.0034789659 -0.25247202 0.25247202 -0.28609717 0.28609717
580000 6.8647484e-06 -0.0034843545 -0.28625495 0.28625495 -0.27985701 0.27985701
590000 8.5391931e-06 -0.003490411 -0.31926339 0.31926339 -0.2731249 0.2731249
600000 1.0347171e-05 -0.0034971194 -0.35144026 0.35144026 -0.2659288 0.2659288
610000 1.2271792e-05 -0.0035044627 -0.38273192 0.38273192 -0.25829822 0.25829822
620000 1.429567e-05 -0.0035124225 -0.41308835 0.41308835 -0.25026402 0.25026402
630000 1.6401103e-05 -0.0035209797 -0.44246327 0.44246327 -0.24185823 0.24185823
640000 1.8570255e-05 -0.0035301142 -0.47081428 0.47081428 -0.23311393 0.23311393
650000 2.078533e-05 -0.0035398052 -0.498103 0.498103 -0.22406507 0.22406507
660000 2.3028745e-05 -0.003550031 -0.52429514 0.52429514 -0.21474628 0.21474628
670000 2.5283288e-05 -0.0035607695 -0.54936056 0.54936056 -0.20519274 0.20519274
680000 2.7532278e-05 -0.0035719977 -0.57327337 0.57327337 -0.19544002 0.19544002
690000 2.9759697e-05 -0.0035836926 -0.59601193 0.59601193 -0.18552392 0.18552392
700000 3.1950329e-05 -0.0035958303 -0.61755887 0.61755887 -0.17548034 0.17548034
710000 3.408987e-05 -0.0036083869 -0.63790112 0.63790112 -0.16534511 0.16534511
720000 3.6165032e-05 -0.0036213382 -0.65702988 0.65702988 -0.15515392 0.15515392
730000 3.8163631e-05 -0.00363466 -0.67494058 0.67494058 -0.14494218 0.14494218
740000 4.0074659e-05 -0.0036483277 -0.69163285 0.69163285 -0.13474489 0.13474489
750000 4.1888343e-05 -0.0036623172 -0.7071105 0.7071105 -0.1245966 0.1245966
760000 4.3596185e-05 -0.0036766041 -0.7213814 0.7213814 -0.11453133 0.11453133
770000 4.5190996e-05 -0.0036911645 -0.73445747 0.73445747 -0.1045825 0.1045825
780000 4.6666906e-05 -0.0037059745 -0.74635458 0.74635458 -0.094782939 0.094782939
790000 4.8019368e-05 -0.0037210109 -0.75709246 0.75709246 -0.085164857 0.085164857
800000 4.9245153e-05 -0.0037362507 -0.76669467 0.76669467 -0.075759891 0.075759891
810000 5.0342325e-05 -0.0037516713 -0.77518852 0.77518852 -0.066599178 0.066599178
820000 5.1310215e-05 -0.003767251 -0.78260499 0.78260499 -0.057713474 0.057713474
830000 5.2149388e-05 -0.0037829686 -0.78897875 0.78897875 -0.049133335 0.049133335
840000 5.2861601e-05 -0.0037988035 -0.79434809 0.79434809 -0.040889384 0.040889384
850000 5.3449761e-05 -0.0038147361 -0.79875498 0.79875498 -0.03301269 0.03301269
860000 5.3917883e-05 -0.0038307476 -0.80224517 0.80224517 -0.025535302 0.025535302
870000 5.4271056e-05 -0.0038468201 -0.80486832 0.80486832 -0.018491033 0.018491033
880000 5.4515415e-05 -0.0038629369 -0.80667827 0.80667827 -0.011916591 0.011916591
890000 5.4658137e-05 -0.0038790822 -0.80773352 0.80773352 -0.00585333 0.00585333
900000 5.4707463e-05 -0.0038952416 -0.80809791 0.80809791 -0.00035001143 0.00035001143
910000 5.4672786e-05 -0.003911402 -0.80784176 0.80784176 0.0045325009 -0.0045325009
920000 5.4564826e-05 -0.0039275517 -0.80704376 0.80704376 0.0087126344 -0.0087126344
930000 5.4396015e-05 -0.0039436807 -0.80579439 0.80579439 0.012070422 -0.012070422
940000 5.4181322e-05 -0.0039597811 -0.80420264 0.80420264 0.014404618 -0.014404618
950000 5.3940325e-05 -0.0039758475 -0.80241211 0.80241211 0.015295834 -0.015295834
960000 5.3704817e-05 -0.0039918778 -0.8006585 0.8006585 0.013305187 -0.013305187
970000 5.3616513e-05 -0.0040078808 -0.79999999 0.79999999 0 0
980000 5.3616513e-05 -0.0040238808 -0.79999999 0.79999999 0 0
990000 5.3616513e-05 -0.0040398808 -0.79999999 0.79999999 0 0
1000000 5.3616513e-05 -0.0040558808 -0.79999999 0.79999999 0 0
Loop time of 0.572025 on 1 procs for 1000000 steps with 2 atoms
99.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1248 | 0.1248 | 0.1248 | 0.0 | 21.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.21166 | 0.21166 | 0.21166 | 0.0 | 37.00
Output | 0.00057419 | 0.00057419 | 0.00057419 | 0.0 | 0.10
Modify | 0.12695 | 0.12695 | 0.12695 | 0.0 | 22.19
Other | | 0.108 | | | 18.89
Nlocal: 2 ave 2 max 2 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: 1 ave 1 max 1 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1
Ave neighs/atom = 0.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

795
examples/granular/log.4Feb25.tableting.200.g++.1 Normal file
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@ -0,0 +1,795 @@
LAMMPS (4 Feb 2025 - Development - patch_5May2020-22356-g0c29a0a0c9-modified)
##################################### SIMULATION SETTINGS ###################################################
atom_style sphere 1
atom_modify map array
comm_modify vel yes
units si
newton off
neighbor 1.0e-3 bin
neigh_modify every 10 delay 60 check no
timestep 4e-6
#processors 2 2 1
############################## SIMULATION BOUNDING BOX AND INSERT PARTICLES #################################
boundary f f f
read_data spheres200.data
Reading data file ...
orthogonal box = (-0.005 -0.005 -0.001) to (0.005 0.005 0.02)
1 by 1 by 1 MPI processor grid
reading atoms ...
200 atoms
read_data CPU = 0.024 seconds
#################################### ADD DIE AND ATOM PARAMETERIZATION ######################################
variable atomRadius equal 0.44e-3*1.25
variable atomDiameter equal 2*${atomRadius}
variable atomDiameter equal 2*0.00055
variable atomDensity equal 1560
variable atomMassAvg equal ${atomDensity}*4.0/3.0*PI*${atomRadius}^3.0
variable atomMassAvg equal 1560*4.0/3.0*PI*${atomRadius}^3.0
variable atomMassAvg equal 1560*4.0/3.0*PI*0.00055^3.0
variable dieRadius equal 4e-3
variable dieHeight equal 1e-2
############################## PARTICLE MATERIAL PROPERTIES AND FORCE MODEL ##################################
pair_style granular
# mdr = E, nu, Y, gamma, psi_b, damp
variable YoungsModulus equal 5e6
variable YieldStress equal 1.9e5
variable PoissonsRatio equal 0.4
variable SurfaceEnergy equal 2
variable SurfaceEnergyWall equal 0.0
variable psi_b equal 0.5
variable damp equal 0.2
variable damp_type equal 1
# linear_history = k_t, x_gammat, mu_s
variable kt equal 2/7*${YoungsModulus}*${atomRadius}
variable kt equal 2/7*5000000*${atomRadius}
variable kt equal 2/7*5000000*0.00055
variable kt_wall equal 2/7*${YoungsModulus}*${atomRadius}
variable kt_wall equal 2/7*5000000*${atomRadius}
variable kt_wall equal 2/7*5000000*0.00055
variable xgammat equal 1.0
variable mu_s equal 0.7
variable mu_s_wall equal 0.1
# sds = mu_roll, k_roll, gamma_roll
variable mu_roll equal 0.6
variable k_roll equal 2.25*${mu_roll}*${mu_roll}*${YoungsModulus}*${atomRadius}
variable k_roll equal 2.25*0.6*${mu_roll}*${YoungsModulus}*${atomRadius}
variable k_roll equal 2.25*0.6*0.6*${YoungsModulus}*${atomRadius}
variable k_roll equal 2.25*0.6*0.6*5000000*${atomRadius}
variable k_roll equal 2.25*0.6*0.6*5000000*0.00055
variable gamma_roll equal 0.0
pair_coeff * * mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 0.5 ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 0.5 0.2 damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 0.5 0.2 damping mdr 1 tangential linear_history ${kt} ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 ${xgammat} ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 ${mu_s} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.7 rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.7 rolling sds 2227.5 ${gamma_roll} ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.7 rolling sds 2227.5 0 ${mu_roll}
pair_coeff * * mdr 5000000 0.4 190000 2 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.7 rolling sds 2227.5 0 0.6
######################################### ADD DIE AND PUNCH WALLS ############################################
variable disp_upper equal 0.0
variable disp_lower equal 0.0
variable wall_contact_string string "granular mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergyWall} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}"
granular mdr 5000000 ${PoissonsRatio} ${YieldStress} ${SurfaceEnergyWall} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 ${YieldStress} ${SurfaceEnergyWall} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 ${SurfaceEnergyWall} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 0 ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 0 0.5 ${damp} damping mdr ${damp_type} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr ${damp_type} tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history ${kt_wall} ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 ${xgammat} ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 ${mu_s_wall} rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.1 rolling sds ${k_roll} ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.1 rolling sds 2227.5 ${gamma_roll} ${mu_roll}
granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.1 rolling sds 2227.5 0 ${mu_roll}
granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.1 rolling sds 2227.5 0 0.6
variable dieHeight2 equal 2*${dieHeight}
variable dieHeight2 equal 2*0.01
region lowerPunch plane 0 0 0 0 0 1 side in units box move NULL NULL v_disp_lower units box
region upperPunch plane 0 0 ${dieHeight} 0 0 -1 side in move NULL NULL v_disp_upper units box
region upperPunch plane 0 0 0.01 0 0 -1 side in move NULL NULL v_disp_upper units box
region die cylinder z 0 0 ${dieRadius} 0 ${dieHeight2} side in units box
region die cylinder z 0 0 0.004 0 ${dieHeight2} side in units box
region die cylinder z 0 0 0.004 0 0.02 side in units box
fix lowerPunch all wall/gran/region ${wall_contact_string} region lowerPunch contacts
fix lowerPunch all wall/gran/region granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.1 rolling sds 2227.5 0 0.6 region lowerPunch contacts
fix upperPunch all wall/gran/region ${wall_contact_string} region upperPunch contacts
fix upperPunch all wall/gran/region granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.1 rolling sds 2227.5 0 0.6 region upperPunch contacts
fix die all wall/gran/region ${wall_contact_string} region die contacts
fix die all wall/gran/region granular mdr 5000000 0.4 190000 0 0.5 0.2 damping mdr 1 tangential linear_history 785.714285714286 1 0.1 rolling sds 2227.5 0 0.6 region die contacts
compute avgUpperPunchForce all reduce sum f_upperPunch[4]
variable avgUpperPunchForce equal c_avgUpperPunchForce
compute avgLowerPunchForce all reduce sum f_lowerPunch[4]
variable avgLowerPunchForce equal c_avgLowerPunchForce
#fix printFD all print 1 "${disp_upper} ${avgUpperPunchForce} ${avgLowerPunchForce}" file punch_force_disp_tableting200.csv screen no
##################################### INTEGRATION AND GRAVITY #################################################
fix 1 all nve/sphere
fix grav all gravity 9.81 vector 0 0 -1
########################################### SCREEN OUTPUT ####################################################
compute 1 all erotate/sphere
thermo_style custom dt step atoms ke vol v_disp_upper
thermo 100
thermo_modify lost ignore norm no
##################################### SET UP DUMP OUTPUTS ####################################################
compute ke all ke/atom
variable output_rate equal round(1e-3/dt)
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- MDR contact model command: (i) https://doi.org/10.1016/j.jmps.2023.105492 || (ii) https://doi.org/10.1016/j.jmps.2023.105493 || (iii) https://doi.org/10.31224/4289
@Article{zunker2024mechanicallyI,
author = {Zunker, William and Kamrin, Ken},
title = {A mechanically-derived contact model for adhesive elastic-perfectly plastic particles,
Part I: Utilizing the method of dimensionality reduction},
journal = {Journal of the Mechanics and Physics of Solids},
year = {2024},
volume = {183},
pages = {105492},
}
@Article{zunker2024mechanicallyII,
author = {Zunker, William and Kamrin, Ken},
title = {A mechanically-derived contact model for adhesive elastic-perfectly plastic particles,
Part II: Contact under high compaction—modeling a bulk elastic response},
journal = {Journal of the Mechanics and Physics of Solids},
year = {2024},
volume = {183},
pages = {105493},
}
@Article{zunker2025experimentally,
author = {Zunker, William and Dunatunga, Sachith and Thakur, Subhash and Tang, Pingjun and Kamrin, Ken},
title = {Experimentally validated DEM for large deformation powder compaction:
mechanically-derived contact model and screening of non-physical contacts},
journal = {Powder Technology},
year = {2025},
pages = {120972},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 10 steps, delay = 60 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.002318
ghost atom cutoff = 0.002318
binsize = 0.001159, bins = 9 9 19
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/atomonly/newtoff
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 72.3 | 72.3 | 72.3 Mbytes
Dt Step Atoms KinEng Volume v_disp_upper
4e-06 0 200 0 2.1e-06 0
Loop time of 7.43e-07 on 1 procs for 0 steps with 200 atoms
134.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 7.43e-07 | | |100.00
Nlocal: 200 ave 200 max 200 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: 1341 ave 1341 max 1341 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1341
Ave neighs/atom = 6.705
Neighbor list builds = 0
Dangerous builds not checked
compute sigmaxx all property/atom d_sigmaxx
compute sigmayy all property/atom d_sigmayy
compute sigmazz all property/atom d_sigmazz
compute Velas all property/atom d_Velas
compute sigmaxx_ave all reduce ave c_sigmaxx
compute sigmayy_ave all reduce ave c_sigmayy
compute sigmazz_ave all reduce ave c_sigmazz
compute Velas_sum all reduce sum c_Velas
variable sxx_ave equal c_sigmaxx_ave
variable syy_ave equal c_sigmayy_ave
variable szz_ave equal c_sigmazz_ave
variable Vparticles equal c_Velas_sum
#fix log all print 1 "${sxx_ave} ${syy_ave} ${szz_ave} ${Vparticles}" file average_normal_stresses_tableting200.csv screen no
#dump dumpParticles all custom ${output_rate} tableting200.dump id type mass diameter x y z vx vy vz fx fy fz c_ke c_sigmaxx c_sigmayy c_sigmazz
#dump dumpParticlesVTK all vtk ${output_rate} post/particles_*.vtk id x y z fx fy fz vx vy vz c_ke radius c_sigmaxx c_sigmayy c_sigmazz
############################################## RUN SIMULATION #################################################
variable upper_punch_stroke equal 0.7*${dieHeight}
variable upper_punch_stroke equal 0.7*0.01
variable vel_upper equal 0.25
variable settling_steps equal round(0.02/dt)
variable compression_steps equal 2*round(${upper_punch_stroke}/${vel_upper}/dt)
variable compression_steps equal 2*round(0.007/${vel_upper}/dt)
variable compression_steps equal 2*round(0.007/0.25/dt)
variable ejection_steps equal ${compression_steps}
variable ejection_steps equal 14000
variable free_float_steps equal round(0.02/dt)
##### SETTLING #####
run ${settling_steps}
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 72.3 | 72.3 | 72.3 Mbytes
Dt Step Atoms KinEng Volume v_disp_upper
4e-06 0 200 0 2.1e-06 0
4e-06 100 200 1.5945503e-09 2.1e-06 0
4e-06 200 200 6.3750614e-09 2.1e-06 0
4e-06 300 200 1.4225143e-08 2.1e-06 0
4e-06 400 200 2.5255561e-08 2.1e-06 0
4e-06 500 200 3.947508e-08 2.1e-06 0
4e-06 600 200 5.6839079e-08 2.1e-06 0
4e-06 700 200 7.7346494e-08 2.1e-06 0
4e-06 800 200 1.0075645e-07 2.1e-06 0
4e-06 900 200 1.2660105e-07 2.1e-06 0
4e-06 1000 200 1.5571123e-07 2.1e-06 0
4e-06 1100 200 1.8785107e-07 2.1e-06 0
4e-06 1200 200 2.2200974e-07 2.1e-06 0
4e-06 1300 200 2.6009223e-07 2.1e-06 0
4e-06 1400 200 3.0148646e-07 2.1e-06 0
4e-06 1500 200 3.4269724e-07 2.1e-06 0
4e-06 1600 200 3.8502938e-07 2.1e-06 0
4e-06 1700 200 4.2763891e-07 2.1e-06 0
4e-06 1800 200 4.6779321e-07 2.1e-06 0
4e-06 1900 200 5.1285578e-07 2.1e-06 0
4e-06 2000 200 5.6630973e-07 2.1e-06 0
4e-06 2100 200 6.1904302e-07 2.1e-06 0
4e-06 2200 200 6.7462868e-07 2.1e-06 0
4e-06 2300 200 7.3066636e-07 2.1e-06 0
4e-06 2400 200 7.7407334e-07 2.1e-06 0
4e-06 2500 200 8.3353557e-07 2.1e-06 0
4e-06 2600 200 9.0017986e-07 2.1e-06 0
4e-06 2700 200 9.5154909e-07 2.1e-06 0
4e-06 2800 200 1.0110977e-06 2.1e-06 0
4e-06 2900 200 1.0661364e-06 2.1e-06 0
4e-06 3000 200 1.1226841e-06 2.1e-06 0
4e-06 3100 200 1.1703917e-06 2.1e-06 0
4e-06 3200 200 1.2254551e-06 2.1e-06 0
4e-06 3300 200 1.2239859e-06 2.1e-06 0
4e-06 3400 200 1.273437e-06 2.1e-06 0
4e-06 3500 200 1.3357598e-06 2.1e-06 0
4e-06 3600 200 1.3949477e-06 2.1e-06 0
4e-06 3700 200 1.459988e-06 2.1e-06 0
4e-06 3800 200 1.5053806e-06 2.1e-06 0
4e-06 3900 200 1.4952453e-06 2.1e-06 0
4e-06 4000 200 1.5037857e-06 2.1e-06 0
4e-06 4100 200 1.5225204e-06 2.1e-06 0
4e-06 4200 200 1.5375323e-06 2.1e-06 0
4e-06 4300 200 1.5552328e-06 2.1e-06 0
4e-06 4400 200 1.581097e-06 2.1e-06 0
4e-06 4500 200 1.6066427e-06 2.1e-06 0
4e-06 4600 200 1.6061944e-06 2.1e-06 0
4e-06 4700 200 1.6110891e-06 2.1e-06 0
4e-06 4800 200 1.6072997e-06 2.1e-06 0
4e-06 4900 200 1.5907992e-06 2.1e-06 0
4e-06 5000 200 1.5501104e-06 2.1e-06 0
Loop time of 0.592588 on 1 procs for 5000 steps with 200 atoms
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20465 | 0.20465 | 0.20465 | 0.0 | 34.53
Neigh | 0.013252 | 0.013252 | 0.013252 | 0.0 | 2.24
Comm | 0.00037594 | 0.00037594 | 0.00037594 | 0.0 | 0.06
Output | 0.00037454 | 0.00037454 | 0.00037454 | 0.0 | 0.06
Modify | 0.37295 | 0.37295 | 0.37295 | 0.0 | 62.93
Other | | 0.0009914 | | | 0.17
Nlocal: 200 ave 200 max 200 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: 1632 ave 1632 max 1632 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1632
Ave neighs/atom = 8.16
Neighbor list builds = 83
Dangerous builds not checked
##### Compression & Release #####
variable punch_frequency equal PI/2/(dt*${compression_steps}/2)
variable punch_frequency equal PI/2/(dt*14000/2)
variable disp_upper equal -${upper_punch_stroke}*sin(${punch_frequency}*elapsed*dt)
variable disp_upper equal -0.007*sin(${punch_frequency}*elapsed*dt)
variable disp_upper equal -0.007*sin(56.0998688141035*elapsed*dt)
variable short_release equal round(${compression_steps}*1.0)
variable short_release equal round(14000*1.0)
run ${short_release}
run 14000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 72.3 | 72.3 | 72.3 Mbytes
Dt Step Atoms KinEng Volume v_disp_upper
4e-06 5000 200 1.5501104e-06 2.1e-06 0
4e-06 5100 200 1.5146077e-06 2.1e-06 -0.00015706645
4e-06 5200 200 1.4902158e-06 2.1e-06 -0.00031405381
4e-06 5300 200 1.3871134e-06 2.1e-06 -0.00047088304
4e-06 5400 200 1.3531184e-06 2.1e-06 -0.00062747516
4e-06 5500 200 1.3154278e-06 2.1e-06 -0.00078375133
4e-06 5600 200 1.2461265e-06 2.1e-06 -0.00093963286
4e-06 5700 200 1.1840322e-06 2.1e-06 -0.0010950413
4e-06 5800 200 1.083844e-06 2.1e-06 -0.0012498983
4e-06 5900 200 9.8572649e-07 2.1e-06 -0.0014041259
4e-06 6000 200 8.6605656e-07 2.1e-06 -0.0015576465
4e-06 6100 200 7.6694391e-07 2.1e-06 -0.0017103828
4e-06 6200 200 7.1292979e-07 2.1e-06 -0.0018622579
4e-06 6300 200 6.475067e-07 2.1e-06 -0.0020131953
4e-06 6400 200 5.378202e-07 2.1e-06 -0.002163119
4e-06 6500 200 4.5668598e-07 2.1e-06 -0.0023119534
4e-06 6600 200 3.1208987e-07 2.1e-06 -0.0024596238
4e-06 6700 200 2.2996407e-07 2.1e-06 -0.0026060556
4e-06 6800 200 1.658813e-07 2.1e-06 -0.0027511752
4e-06 6900 200 1.4495016e-07 2.1e-06 -0.0028949095
4e-06 7000 200 1.6172966e-07 2.1e-06 -0.0030371862
4e-06 7100 200 4.6620591e-07 2.1e-06 -0.0031779335
4e-06 7200 200 6.8121833e-07 2.1e-06 -0.0033170806
4e-06 7300 200 1.5506154e-06 2.1e-06 -0.0034545575
4e-06 7400 200 2.5919669e-06 2.1e-06 -0.0035902949
4e-06 7500 200 2.9403576e-06 2.1e-06 -0.0037242245
4e-06 7600 200 2.7726732e-06 2.1e-06 -0.0038562789
4e-06 7700 200 2.6586936e-06 2.1e-06 -0.0039863915
4e-06 7800 200 2.7059447e-06 2.1e-06 -0.0041144968
4e-06 7900 200 2.8454301e-06 2.1e-06 -0.0042405303
4e-06 8000 200 2.7747574e-06 2.1e-06 -0.0043644286
4e-06 8100 200 2.6329747e-06 2.1e-06 -0.0044861293
4e-06 8200 200 2.3654294e-06 2.1e-06 -0.0046055711
4e-06 8300 200 2.616465e-06 2.1e-06 -0.0047226938
4e-06 8400 200 2.6920973e-06 2.1e-06 -0.0048374385
4e-06 8500 200 2.6041158e-06 2.1e-06 -0.0049497475
4e-06 8600 200 1.8236056e-06 2.1e-06 -0.005059564
4e-06 8700 200 2.1290462e-06 2.1e-06 -0.005166833
4e-06 8800 200 1.8723934e-06 2.1e-06 -0.0052715003
4e-06 8900 200 1.7196474e-06 2.1e-06 -0.0053735132
4e-06 9000 200 1.558001e-06 2.1e-06 -0.0054728204
4e-06 9100 200 1.1714433e-06 2.1e-06 -0.0055693718
4e-06 9200 200 1.7973167e-06 2.1e-06 -0.005663119
4e-06 9300 200 1.4951874e-06 2.1e-06 -0.0057540145
4e-06 9400 200 1.197557e-06 2.1e-06 -0.0058420128
4e-06 9500 200 1.1638085e-06 2.1e-06 -0.0059270694
4e-06 9600 200 1.2591061e-06 2.1e-06 -0.0060091416
4e-06 9700 200 1.2747299e-06 2.1e-06 -0.0060881879
4e-06 9800 200 1.2424243e-06 2.1e-06 -0.0061641687
4e-06 9900 200 1.1624586e-06 2.1e-06 -0.0062370457
4e-06 10000 200 1.0724272e-06 2.1e-06 -0.0063067821
4e-06 10100 200 1.0806622e-06 2.1e-06 -0.0063733428
4e-06 10200 200 9.2046484e-07 2.1e-06 -0.0064366944
4e-06 10300 200 8.1801156e-07 2.1e-06 -0.0064968049
4e-06 10400 200 7.74927e-07 2.1e-06 -0.0065536441
4e-06 10500 200 6.85447e-07 2.1e-06 -0.0066071833
4e-06 10600 200 5.4693931e-07 2.1e-06 -0.0066573956
4e-06 10700 200 4.5275522e-07 2.1e-06 -0.0067042557
4e-06 10800 200 4.2807826e-07 2.1e-06 -0.00674774
4e-06 10900 200 3.5676739e-07 2.1e-06 -0.0067878266
4e-06 11000 200 2.9448839e-07 2.1e-06 -0.0068244954
4e-06 11100 200 2.7397196e-07 2.1e-06 -0.0068577278
4e-06 11200 200 1.8313029e-07 2.1e-06 -0.0068875071
4e-06 11300 200 1.4616679e-07 2.1e-06 -0.0069138184
4e-06 11400 200 1.0916404e-07 2.1e-06 -0.0069366483
4e-06 11500 200 7.4608897e-08 2.1e-06 -0.0069559855
4e-06 11600 200 4.9799693e-08 2.1e-06 -0.0069718201
4e-06 11700 200 2.996701e-08 2.1e-06 -0.0069841441
4e-06 11800 200 1.1810054e-08 2.1e-06 -0.0069929515
4e-06 11900 200 3.9455661e-09 2.1e-06 -0.0069982376
4e-06 12000 200 7.0818836e-11 2.1e-06 -0.007
4e-06 12100 200 3.989114e-09 2.1e-06 -0.0069982376
4e-06 12200 200 1.0481589e-08 2.1e-06 -0.0069929515
4e-06 12300 200 2.3561653e-08 2.1e-06 -0.0069841441
4e-06 12400 200 4.1819363e-08 2.1e-06 -0.0069718201
4e-06 12500 200 6.5328826e-08 2.1e-06 -0.0069559855
4e-06 12600 200 9.3738095e-08 2.1e-06 -0.0069366483
4e-06 12700 200 1.3058219e-07 2.1e-06 -0.0069138184
4e-06 12800 200 1.7668602e-07 2.1e-06 -0.0068875071
4e-06 12900 200 2.1482809e-07 2.1e-06 -0.0068577278
4e-06 13000 200 2.7185589e-07 2.1e-06 -0.0068244954
4e-06 13100 200 3.3577426e-07 2.1e-06 -0.0067878266
4e-06 13200 200 3.9749034e-07 2.1e-06 -0.00674774
4e-06 13300 200 5.0743398e-07 2.1e-06 -0.0067042557
4e-06 13400 200 5.6629069e-07 2.1e-06 -0.0066573956
4e-06 13500 200 5.9092105e-07 2.1e-06 -0.0066071833
4e-06 13600 200 7.313638e-07 2.1e-06 -0.0065536441
4e-06 13700 200 1.0954352e-06 2.1e-06 -0.0064968049
4e-06 13800 200 7.1637332e-07 2.1e-06 -0.0064366944
4e-06 13900 200 8.5398051e-07 2.1e-06 -0.0063733428
4e-06 14000 200 1.0429888e-06 2.1e-06 -0.0063067821
4e-06 14100 200 1.6673022e-07 2.1e-06 -0.0062370457
4e-06 14200 200 2.0206568e-08 2.1e-06 -0.0061641687
4e-06 14300 200 5.6062261e-09 2.1e-06 -0.0060881879
4e-06 14400 200 4.5198973e-09 2.1e-06 -0.0060091416
4e-06 14500 200 2.5522353e-09 2.1e-06 -0.0059270694
4e-06 14600 200 9.091094e-10 2.1e-06 -0.0058420128
4e-06 14700 200 1.3992806e-10 2.1e-06 -0.0057540145
4e-06 14800 200 1.0208666e-11 2.1e-06 -0.005663119
4e-06 14900 200 8.4078334e-11 2.1e-06 -0.0055693718
4e-06 15000 200 1.2567311e-10 2.1e-06 -0.0054728204
4e-06 15100 200 5.2285722e-10 2.1e-06 -0.0053735132
4e-06 15200 200 1.5839179e-10 2.1e-06 -0.0052715003
4e-06 15300 200 3.2283374e-11 2.1e-06 -0.005166833
4e-06 15400 200 2.9516435e-12 2.1e-06 -0.005059564
4e-06 15500 200 1.0302118e-11 2.1e-06 -0.0049497475
4e-06 15600 200 1.7289975e-11 2.1e-06 -0.0048374385
4e-06 15700 200 1.4850209e-11 2.1e-06 -0.0047226938
4e-06 15800 200 8.0260964e-12 2.1e-06 -0.0046055711
4e-06 15900 200 2.616591e-12 2.1e-06 -0.0044861293
4e-06 16000 200 3.0793261e-13 2.1e-06 -0.0043644286
4e-06 16100 200 4.9187696e-13 2.1e-06 -0.0042405303
4e-06 16200 200 3.9849142e-13 2.1e-06 -0.0041144968
4e-06 16300 200 5.2823345e-13 2.1e-06 -0.0039863915
4e-06 16400 200 3.9902725e-13 2.1e-06 -0.0038562789
4e-06 16500 200 1.9259043e-13 2.1e-06 -0.0037242245
4e-06 16600 200 5.3557316e-14 2.1e-06 -0.0035902949
4e-06 16700 200 3.7734621e-15 2.1e-06 -0.0034545575
4e-06 16800 200 3.0867115e-15 2.1e-06 -0.0033170806
4e-06 16900 200 1.1841579e-14 2.1e-06 -0.0031779335
4e-06 17000 200 1.3850503e-14 2.1e-06 -0.0030371862
4e-06 17100 200 9.8491914e-15 2.1e-06 -0.0028949095
4e-06 17200 200 4.7140149e-15 2.1e-06 -0.0027511752
4e-06 17300 200 1.3440466e-15 2.1e-06 -0.0026060556
4e-06 17400 200 1.0627828e-16 2.1e-06 -0.0024596238
4e-06 17500 200 6.2015781e-17 2.1e-06 -0.0023119534
4e-06 17600 200 2.8723007e-16 2.1e-06 -0.002163119
4e-06 17700 200 3.6601367e-16 2.1e-06 -0.0020131953
4e-06 17800 200 2.7862312e-16 2.1e-06 -0.0018622579
4e-06 17900 200 1.4268051e-16 2.1e-06 -0.0017103828
4e-06 18000 200 4.5443603e-17 2.1e-06 -0.0015576465
4e-06 18100 200 5.2330376e-18 2.1e-06 -0.0014041259
4e-06 18200 200 7.3566254e-19 2.1e-06 -0.0012498983
4e-06 18300 200 6.5880468e-18 2.1e-06 -0.0010950413
4e-06 18400 200 9.5744931e-18 2.1e-06 -0.00093963286
4e-06 18500 200 7.8604487e-18 2.1e-06 -0.00078375133
4e-06 18600 200 4.3166295e-18 2.1e-06 -0.00062747516
4e-06 18700 200 1.5188792e-18 2.1e-06 -0.00047088304
4e-06 18800 200 2.3221067e-19 2.1e-06 -0.00031405381
4e-06 18900 200 4.7558964e-21 2.1e-06 -0.00015706645
4e-06 19000 200 1.4567292e-19 2.1e-06 2.0903119e-17
Loop time of 6.96616 on 1 procs for 14000 steps with 200 atoms
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.8534 | 3.8534 | 3.8534 | 0.0 | 55.32
Neigh | 0.038778 | 0.038778 | 0.038778 | 0.0 | 0.56
Comm | 0.0015081 | 0.0015081 | 0.0015081 | 0.0 | 0.02
Output | 0.0018007 | 0.0018007 | 0.0018007 | 0.0 | 0.03
Modify | 3.0668 | 3.0668 | 3.0668 | 0.0 | 44.02
Other | | 0.003851 | | | 0.06
Nlocal: 200 ave 200 max 200 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: 3031 ave 3031 max 3031 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3031
Ave neighs/atom = 15.155
Neighbor list builds = 233
Dangerous builds not checked
##### EJECTION #####
variable punch_frequency equal PI/2/(dt*${ejection_steps})
variable punch_frequency equal PI/2/(dt*14000)
variable disp_lower equal ${dieHeight}*sin(${punch_frequency}*elapsed*dt)
variable disp_lower equal 0.01*sin(${punch_frequency}*elapsed*dt)
variable disp_lower equal 0.01*sin(28.0499344070517*elapsed*dt)
variable disp_upper equal 0.9*v_disp_lower
run ${ejection_steps}
run 14000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 72.31 | 72.31 | 72.31 Mbytes
Dt Step Atoms KinEng Volume v_disp_upper
4e-06 19000 200 1.4567292e-19 2.1e-06 0
4e-06 19100 200 1.9132195e-05 2.1e-06 0.00010097765
4e-06 19200 200 3.1561748e-06 2.1e-06 0.00020194258
4e-06 19300 200 1.4462178e-05 2.1e-06 0.00030288209
4e-06 19400 200 4.6622112e-06 2.1e-06 0.00040378347
4e-06 19500 200 1.1929852e-05 2.1e-06 0.00050463403
4e-06 19600 200 5.6933661e-06 2.1e-06 0.00060542105
4e-06 19700 200 1.0429976e-05 2.1e-06 0.00070613186
4e-06 19800 200 6.6580254e-06 2.1e-06 0.00080675378
4e-06 19900 200 9.1721686e-06 2.1e-06 0.00090727414
4e-06 20000 200 7.4553343e-06 2.1e-06 0.0010076803
4e-06 20100 200 8.3534813e-06 2.1e-06 0.0011079596
4e-06 20200 200 7.8671075e-06 2.1e-06 0.0012080994
4e-06 20300 200 7.9115898e-06 2.1e-06 0.0013080871
4e-06 20400 200 8.2222312e-06 2.1e-06 0.0014079102
4e-06 20500 200 7.5281175e-06 2.1e-06 0.001507556
4e-06 20600 200 8.4242027e-06 2.1e-06 0.0016070121
4e-06 20700 200 7.3282364e-06 2.1e-06 0.0017062658
4e-06 20800 200 8.3501222e-06 2.1e-06 0.0018053047
4e-06 20900 200 7.3417566e-06 2.1e-06 0.0019041164
4e-06 21000 200 8.0702927e-06 2.1e-06 0.0020026884
4e-06 21100 200 7.5896194e-06 2.1e-06 0.0021010083
4e-06 21200 200 7.6596342e-06 2.1e-06 0.0021990637
4e-06 21300 200 7.7009755e-06 2.1e-06 0.0022968422
4e-06 21400 200 7.4010568e-06 2.1e-06 0.0023943316
4e-06 21500 200 7.7254953e-06 2.1e-06 0.0024915196
4e-06 21600 200 7.2931076e-06 2.1e-06 0.0025883939
4e-06 21700 200 7.5667043e-06 2.1e-06 0.0026849424
4e-06 21800 200 7.2767179e-06 2.1e-06 0.0027811529
4e-06 21900 200 7.3632148e-06 2.1e-06 0.0028770133
4e-06 22000 200 7.2563523e-06 2.1e-06 0.0029725116
4e-06 22100 200 7.2003226e-06 2.1e-06 0.0030676356
4e-06 22200 200 7.1862422e-06 2.1e-06 0.0031623734
4e-06 22300 200 7.0035785e-06 2.1e-06 0.0032567132
4e-06 22400 200 7.1023437e-06 2.1e-06 0.0033506429
4e-06 22500 200 6.8767896e-06 2.1e-06 0.0034441509
4e-06 22600 200 6.9556381e-06 2.1e-06 0.0035372253
4e-06 22700 200 6.7754491e-06 2.1e-06 0.0036298544
4e-06 22800 200 6.7752923e-06 2.1e-06 0.0037220265
4e-06 22900 200 6.6947789e-06 2.1e-06 0.0038137301
4e-06 23000 200 6.5811876e-06 2.1e-06 0.0039049537
4e-06 23100 200 6.5600064e-06 2.1e-06 0.0039956856
4e-06 23200 200 6.407054e-06 2.1e-06 0.0040859145
4e-06 23300 200 6.4635326e-06 2.1e-06 0.0041756291
4e-06 23400 200 6.2604509e-06 2.1e-06 0.004264818
4e-06 23500 200 6.2914059e-06 2.1e-06 0.00435347
4e-06 23600 200 6.1416598e-06 2.1e-06 0.004441574
4e-06 23700 200 6.0839487e-06 2.1e-06 0.0045291188
4e-06 23800 200 6.0216029e-06 2.1e-06 0.0046160935
4e-06 23900 200 5.896464e-06 2.1e-06 0.0047024871
4e-06 24000 200 5.8682556e-06 2.1e-06 0.0047882887
4e-06 24100 200 5.8744357e-06 2.1e-06 0.0048734875
4e-06 24200 200 5.6172509e-06 2.1e-06 0.0049580728
4e-06 24300 200 5.6527872e-06 2.1e-06 0.005042034
4e-06 24400 200 5.4706998e-06 2.1e-06 0.0051253604
4e-06 24500 200 5.4368713e-06 2.1e-06 0.0052080417
4e-06 24600 200 5.3496195e-06 2.1e-06 0.0052900673
4e-06 24700 200 5.2020248e-06 2.1e-06 0.0053714269
4e-06 24800 200 5.2035809e-06 2.1e-06 0.0054521104
4e-06 24900 200 5.0302031e-06 2.1e-06 0.0055321075
4e-06 25000 200 5.0094633e-06 2.1e-06 0.0056114082
4e-06 25100 200 4.8588064e-06 2.1e-06 0.0056900025
4e-06 25200 200 4.8221437e-06 2.1e-06 0.0057678805
4e-06 25300 200 4.7117322e-06 2.1e-06 0.0058450324
4e-06 25400 200 4.6148719e-06 2.1e-06 0.0059214485
4e-06 25500 200 4.5348297e-06 2.1e-06 0.0059971192
4e-06 25600 200 4.4325937e-06 2.1e-06 0.0060720349
4e-06 25700 200 4.3587865e-06 2.1e-06 0.0061461862
4e-06 25800 200 4.2449842e-06 2.1e-06 0.0062195638
4e-06 25900 200 4.1730814e-06 2.1e-06 0.0062921585
4e-06 26000 200 4.0712085e-06 2.1e-06 0.006363961
4e-06 26100 200 3.9603603e-06 2.1e-06 0.0064349624
4e-06 26200 200 3.9152641e-06 2.1e-06 0.0065051538
4e-06 26300 200 3.7864366e-06 2.1e-06 0.0065745262
4e-06 26400 200 3.7211553e-06 2.1e-06 0.006643071
4e-06 26500 200 3.6038142e-06 2.1e-06 0.0067107795
4e-06 26600 200 3.5518456e-06 2.1e-06 0.0067776432
4e-06 26700 200 3.4213616e-06 2.1e-06 0.0068436537
4e-06 26800 200 3.348649e-06 2.1e-06 0.0069088027
4e-06 26900 200 3.2592054e-06 2.1e-06 0.0069730819
4e-06 27000 200 3.1640896e-06 2.1e-06 0.0070364833
4e-06 27100 200 3.1491467e-06 2.1e-06 0.007098999
4e-06 27200 200 2.9475347e-06 2.1e-06 0.0071606209
4e-06 27300 200 2.9234007e-06 2.1e-06 0.0072213415
4e-06 27400 200 2.8106832e-06 2.1e-06 0.0072811529
4e-06 27500 200 2.7190831e-06 2.1e-06 0.0073400478
4e-06 27600 200 2.6595021e-06 2.1e-06 0.0073980187
4e-06 27700 200 2.5384163e-06 2.1e-06 0.0074550582
4e-06 27800 200 2.4906759e-06 2.1e-06 0.0075111593
4e-06 27900 200 2.3760852e-06 2.1e-06 0.0075663148
4e-06 28000 200 2.3135864e-06 2.1e-06 0.0076205178
4e-06 28100 200 2.206388e-06 2.1e-06 0.0076737615
4e-06 28200 200 2.1580755e-06 2.1e-06 0.0077260391
4e-06 28300 200 2.0541807e-06 2.1e-06 0.0077773442
4e-06 28400 200 1.9879886e-06 2.1e-06 0.0078276702
4e-06 28500 200 1.9080731e-06 2.1e-06 0.0078770108
4e-06 28600 200 1.8244513e-06 2.1e-06 0.0079253598
4e-06 28700 200 1.7612085e-06 2.1e-06 0.0079727111
4e-06 28800 200 1.6725418e-06 2.1e-06 0.0080190587
4e-06 28900 200 1.6108221e-06 2.1e-06 0.0080643969
4e-06 29000 200 1.5315923e-06 2.1e-06 0.0081087198
4e-06 29100 200 1.4668177e-06 2.1e-06 0.008152022
4e-06 29200 200 1.389947e-06 2.1e-06 0.0081942979
4e-06 29300 200 1.3244327e-06 2.1e-06 0.0082355423
4e-06 29400 200 1.2613389e-06 2.1e-06 0.00827575
4e-06 29500 200 1.189317e-06 2.1e-06 0.0083149158
4e-06 29600 200 1.1328651e-06 2.1e-06 0.0083530349
4e-06 29700 200 1.0634003e-06 2.1e-06 0.0083901025
4e-06 29800 200 1.0089659e-06 2.1e-06 0.0084261138
4e-06 29900 200 9.452383e-07 2.1e-06 0.0084610645
4e-06 30000 200 8.8857387e-07 2.1e-06 0.00849495
4e-06 30100 200 8.3934751e-07 2.1e-06 0.0085277661
4e-06 30200 200 7.7404495e-07 2.1e-06 0.0085595086
4e-06 30300 200 7.2760888e-07 2.1e-06 0.0085901737
4e-06 30400 200 6.7239685e-07 2.1e-06 0.0086197574
4e-06 30500 200 6.245416e-07 2.1e-06 0.0086482559
4e-06 30600 200 5.7834155e-07 2.1e-06 0.0086756657
4e-06 30700 200 5.2814574e-07 2.1e-06 0.0087019834
4e-06 30800 200 4.8878902e-07 2.1e-06 0.0087272057
4e-06 30900 200 4.4241206e-07 2.1e-06 0.0087513293
4e-06 31000 200 4.0442514e-07 2.1e-06 0.0087743512
4e-06 31100 200 3.642199e-07 2.1e-06 0.0087962686
4e-06 31200 200 3.2738558e-07 2.1e-06 0.0088170786
4e-06 31300 200 2.9389397e-07 2.1e-06 0.0088367787
4e-06 31400 200 2.5861566e-07 2.1e-06 0.0088553663
4e-06 31500 200 2.2934636e-07 2.1e-06 0.0088728392
4e-06 31600 200 1.9888494e-07 2.1e-06 0.0088891951
4e-06 31700 200 1.7250531e-07 2.1e-06 0.0089044319
4e-06 31800 200 1.4678036e-07 2.1e-06 0.0089185479
4e-06 31900 200 1.2324632e-07 2.1e-06 0.0089315411
4e-06 32000 200 1.0248084e-07 2.1e-06 0.0089434099
4e-06 32100 200 8.2609273e-08 2.1e-06 0.0089541529
4e-06 32200 200 6.551679e-08 2.1e-06 0.0089637686
4e-06 32300 200 5.0080052e-08 2.1e-06 0.008972256
4e-06 32400 200 3.6856646e-08 2.1e-06 0.0089796139
4e-06 32500 200 2.5648284e-08 2.1e-06 0.0089858413
4e-06 32600 200 1.637837e-08 2.1e-06 0.0089909376
4e-06 32700 200 9.2578154e-09 2.1e-06 0.008994902
4e-06 32800 200 4.0824723e-09 2.1e-06 0.0089977341
4e-06 32900 200 1.0371165e-09 2.1e-06 0.0089994335
4e-06 33000 200 6.1012168e-14 2.1e-06 0.009
Loop time of 7.70808 on 1 procs for 14000 steps with 200 atoms
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4414 | 4.4414 | 4.4414 | 0.0 | 57.62
Neigh | 0.040941 | 0.040941 | 0.040941 | 0.0 | 0.53
Comm | 0.001526 | 0.001526 | 0.001526 | 0.0 | 0.02
Output | 0.0019617 | 0.0019617 | 0.0019617 | 0.0 | 0.03
Modify | 3.2183 | 3.2183 | 3.2183 | 0.0 | 41.75
Other | | 0.003942 | | | 0.05
Nlocal: 200 ave 200 max 200 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: 3026 ave 3026 max 3026 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3026
Ave neighs/atom = 15.13
Neighbor list builds = 233
Dangerous builds not checked
##### FREE FLOAT #####
variable disp_lower equal ${dieHeight}
variable disp_lower equal 0.01
variable disp_upper equal ${dieHeight}*0.9
variable disp_upper equal 0.01*0.9
variable max_disp equal ${dieRadius}*0.75
variable max_disp equal 0.004*0.75
run ${free_float_steps}
run 5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 72.31 | 72.31 | 72.31 Mbytes
Dt Step Atoms KinEng Volume v_disp_upper
4e-06 33000 200 6.1012168e-14 2.1e-06 0.009
4e-06 33100 200 6.7902539e-11 2.1e-06 0.009
4e-06 33200 200 2.0896758e-11 2.1e-06 0.009
4e-06 33300 200 2.5200405e-11 2.1e-06 0.009
4e-06 33400 200 2.1747895e-12 2.1e-06 0.009
4e-06 33500 200 1.1228817e-11 2.1e-06 0.009
4e-06 33600 200 3.3597579e-12 2.1e-06 0.009
4e-06 33700 200 1.4808583e-12 2.1e-06 0.009
4e-06 33800 200 3.5132295e-12 2.1e-06 0.009
4e-06 33900 200 8.2438639e-14 2.1e-06 0.009
4e-06 34000 200 1.3267378e-12 2.1e-06 0.009
4e-06 34100 200 6.2365031e-13 2.1e-06 0.009
4e-06 34200 200 1.1820072e-13 2.1e-06 0.009
4e-06 34300 200 5.2797742e-13 2.1e-06 0.009
4e-06 34400 200 3.2199555e-14 2.1e-06 0.009
4e-06 34500 200 1.553388e-13 2.1e-06 0.009
4e-06 34600 200 1.1458173e-13 2.1e-06 0.009
4e-06 34700 200 5.8686124e-15 2.1e-06 0.009
4e-06 34800 200 7.3486748e-14 2.1e-06 0.009
4e-06 34900 200 1.0877367e-14 2.1e-06 0.009
4e-06 35000 200 1.5284442e-14 2.1e-06 0.009
4e-06 35100 200 2.0294057e-14 2.1e-06 0.009
4e-06 35200 200 1.5385334e-17 2.1e-06 0.009
4e-06 35300 200 9.5858898e-15 2.1e-06 0.009
4e-06 35400 200 3.1985384e-15 2.1e-06 0.009
4e-06 35500 200 1.1327574e-15 2.1e-06 0.009
4e-06 35600 200 3.3810722e-15 2.1e-06 0.009
4e-06 35700 200 1.2867327e-16 2.1e-06 0.009
4e-06 35800 200 1.0755232e-15 2.1e-06 0.009
4e-06 35900 200 7.3381985e-16 2.1e-06 0.009
4e-06 36000 200 3.7750251e-17 2.1e-06 0.009
4e-06 36100 200 4.8518794e-16 2.1e-06 0.009
4e-06 36200 200 8.361623e-17 2.1e-06 0.009
4e-06 36300 200 8.9347649e-17 2.1e-06 0.009
4e-06 36400 200 1.4528409e-16 2.1e-06 0.009
4e-06 36500 200 8.2328133e-19 2.1e-06 0.009
4e-06 36600 200 5.9628413e-17 2.1e-06 0.009
4e-06 36700 200 2.857306e-17 2.1e-06 0.009
4e-06 36800 200 4.1078269e-18 2.1e-06 0.009
4e-06 36900 200 2.4094514e-17 2.1e-06 0.009
4e-06 37000 200 2.6153896e-18 2.1e-06 0.009
4e-06 37100 200 5.6577297e-18 2.1e-06 0.009
4e-06 37200 200 6.5849416e-18 2.1e-06 0.009
4e-06 37300 200 4.5596918e-21 2.1e-06 0.009
4e-06 37400 200 3.2329813e-18 2.1e-06 0.009
4e-06 37500 200 1.123288e-18 2.1e-06 0.009
4e-06 37600 200 3.4227094e-19 2.1e-06 0.009
4e-06 37700 200 1.1782135e-18 2.1e-06 0.009
4e-06 37800 200 6.9535961e-20 2.1e-06 0.009
4e-06 37900 200 3.4055174e-19 2.1e-06 0.009
4e-06 38000 200 2.8968649e-19 2.1e-06 0.009
Loop time of 2.65906 on 1 procs for 5000 steps with 200 atoms
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5595 | 1.5595 | 1.5595 | 0.0 | 58.65
Neigh | 0.012904 | 0.012904 | 0.012904 | 0.0 | 0.49
Comm | 0.00041333 | 0.00041333 | 0.00041333 | 0.0 | 0.02
Output | 0.00053486 | 0.00053486 | 0.00053486 | 0.0 | 0.02
Modify | 1.0844 | 1.0844 | 1.0844 | 0.0 | 40.78
Other | | 0.001336 | | | 0.05
Nlocal: 200 ave 200 max 200 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: 3026 ave 3026 max 3026 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3026
Ave neighs/atom = 15.13
Neighbor list builds = 83
Dangerous builds not checked
Total wall time: 0:00:18

784
examples/granular/log.4Feb25.triaxial.compaction.12.g++.1 Normal file
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LAMMPS (4 Feb 2025 - Development - patch_5May2020-22356-g0c29a0a0c9-modified)
############################### SIMULATION SETTINGS ###################################################
atom_style sphere 1
atom_modify map array
comm_modify vel yes
units si
newton off
neighbor 2 bin
neigh_modify delay 0
timestep 1e-6
##################### SIMULATION BOUNDING BOX, INSERT PARTICLES, AND INTEGRATION #######################
boundary f f f
read_data spheres12.data
Reading data file ...
orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
12 atoms
read_data CPU = 0.029 seconds
fix integr all nve/sphere
# create pair group for contact area outputs
group particles_1_12 id 1 12
2 atoms in group particles_1_12
########################### PARTICLE MATERIAL PROPERTIES AND FORCE MODEL ###############################
variable atomRadius equal 0.5
pair_style granular
# mdr = E, nu, Y, gamma, psi_b, damp
variable YoungsModulus equal 1e9
variable PoissonsRatio equal 0.3
variable YieldStress equal 50e6
variable SurfaceEnergy equal 0.0
variable psi_b equal 0.5
variable damp equal 0.2
variable damp_type equal 1
# linear_history = k_t, x_gamma,t, mu_s
variable kt equal 2/7*${YoungsModulus}*${atomRadius}
variable kt equal 2/7*1000000000*${atomRadius}
variable kt equal 2/7*1000000000*0.5
variable xgammat equal 0.0
variable mu_s equal 0.5
pair_coeff * * mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
pair_coeff * * mdr 1000000000 ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
pair_coeff * * mdr 1000000000 0.3 ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
pair_coeff * * mdr 1000000000 0.3 50000000 ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
pair_coeff * * mdr 1000000000 0.3 50000000 0 ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
pair_coeff * * mdr 1000000000 0.3 50000000 0 0.5 ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
pair_coeff * * mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
pair_coeff * * mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history ${kt} ${xgammat} ${mu_s}
pair_coeff * * mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 ${xgammat} ${mu_s}
pair_coeff * * mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 ${mu_s}
pair_coeff * * mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 0.5
######################################### ADD IN PLANES ################################################
variable boxWidth equal 3
variable halfBoxWidth equal ${boxWidth}/2
variable halfBoxWidth equal 3/2
variable plane_disp equal 0.0
variable plane_disp_neg equal 0.0
region plane_yz_pos plane ${halfBoxWidth} 0 0 -1 0 0 side in move v_plane_disp_neg NULL NULL units box
region plane_yz_pos plane 1.5 0 0 -1 0 0 side in move v_plane_disp_neg NULL NULL units box
region plane_yz_neg plane -${halfBoxWidth} 0 0 1 0 0 side in move v_plane_disp NULL NULL units box
region plane_yz_neg plane -1.5 0 0 1 0 0 side in move v_plane_disp NULL NULL units box
region plane_xz_pos plane 0 ${halfBoxWidth} 0 0 -1 0 side in move NULL v_plane_disp_neg NULL units box
region plane_xz_pos plane 0 1.5 0 0 -1 0 side in move NULL v_plane_disp_neg NULL units box
region plane_xz_neg plane 0 -${halfBoxWidth} 0 0 1 0 side in move NULL v_plane_disp NULL units box
region plane_xz_neg plane 0 -1.5 0 0 1 0 side in move NULL v_plane_disp NULL units box
region plane_xy_pos plane 0 0 ${halfBoxWidth} 0 0 -1 side in move NULL NULL v_plane_disp_neg units box
region plane_xy_pos plane 0 0 1.5 0 0 -1 side in move NULL NULL v_plane_disp_neg units box
region plane_xy_neg plane 0 0 -${halfBoxWidth} 0 0 1 side in move NULL NULL v_plane_disp units box
region plane_xy_neg plane 0 0 -1.5 0 0 1 side in move NULL NULL v_plane_disp units box
variable wall_contact_string string "granular mdr ${YoungsModulus} ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s} "
granular mdr 1000000000 ${PoissonsRatio} ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
granular mdr 1000000000 0.3 ${YieldStress} ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
granular mdr 1000000000 0.3 50000000 ${SurfaceEnergy} ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
granular mdr 1000000000 0.3 50000000 0 ${psi_b} ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
granular mdr 1000000000 0.3 50000000 0 0.5 ${damp} damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr ${damp_type} tangential linear_history ${kt} ${xgammat} ${mu_s}
granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history ${kt} ${xgammat} ${mu_s}
granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 ${xgammat} ${mu_s}
granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 ${mu_s}
granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 0.5
fix plane_yz_pos all wall/gran/region ${wall_contact_string} region plane_yz_pos contacts
fix plane_yz_pos all wall/gran/region granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 0.5 region plane_yz_pos contacts
fix plane_yz_neg all wall/gran/region ${wall_contact_string} region plane_yz_neg contacts
fix plane_yz_neg all wall/gran/region granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 0.5 region plane_yz_neg contacts
fix plane_xz_pos all wall/gran/region ${wall_contact_string} region plane_xz_pos contacts
fix plane_xz_pos all wall/gran/region granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 0.5 region plane_xz_pos contacts
fix plane_xz_neg all wall/gran/region ${wall_contact_string} region plane_xz_neg contacts
fix plane_xz_neg all wall/gran/region granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 0.5 region plane_xz_neg contacts
fix plane_xy_pos all wall/gran/region ${wall_contact_string} region plane_xy_pos contacts
fix plane_xy_pos all wall/gran/region granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 0.5 region plane_xy_pos contacts
fix plane_xy_neg all wall/gran/region ${wall_contact_string} region plane_xy_neg contacts
fix plane_xy_neg all wall/gran/region granular mdr 1000000000 0.3 50000000 0 0.5 0.2 damping mdr 1 tangential linear_history 142857142.857143 0 0.5 region plane_xy_neg contacts
compute plane_xy_neg_force all reduce sum f_plane_xy_neg[4]
variable plane_xy_neg_force equal c_plane_xy_neg_force
compute plane_xz_neg_force all reduce sum f_plane_xz_neg[3]
variable plane_xz_neg_force equal c_plane_xz_neg_force
compute plane_yz_neg_force all reduce sum f_plane_yz_neg[2]
variable plane_yz_neg_force equal c_plane_yz_neg_force
#fix print1 all print 1 "${plane_disp} ${plane_xy_neg_force} ${plane_xz_neg_force} ${plane_yz_neg_force}" file force_disp_triaxial12.csv screen no
######################################## SCREEN OUTPUT ####################################################
compute 1 all erotate/sphere
thermo_style custom dt step atoms ke c_1 vol
thermo 100
thermo_modify lost ignore norm no
##################################### DEFINE WALL MOVEMENT #################################################
variable disp_max equal 0.499
variable ddisp equal 0.00001
variable compression_steps equal round(${disp_max}/${ddisp})
variable compression_steps equal round(0.499/${ddisp})
variable compression_steps equal round(0.499/1e-05)
variable output_rate equal round(${compression_steps}/100)
variable output_rate equal round(49900/100)
##################################### SET UP DUMP OUTPUTS ####################################################
#dump dumpParticles all custom ${output_rate} triaxial_compaction_12.dump id type mass x y z vx vy vz fx fy fz radius
#dump dmp all vtk ${output_rate} post/triaxial12particles_*.vtk id type mass x y z vx vy vz fx fy fz radius
#################################### COMPRESS THE PARTICLES ##################################################
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- MDR contact model command: (i) https://doi.org/10.1016/j.jmps.2023.105492 || (ii) https://doi.org/10.1016/j.jmps.2023.105493 || (iii) https://doi.org/10.31224/4289
@Article{zunker2024mechanicallyI,
author = {Zunker, William and Kamrin, Ken},
title = {A mechanically-derived contact model for adhesive elastic-perfectly plastic particles,
Part I: Utilizing the method of dimensionality reduction},
journal = {Journal of the Mechanics and Physics of Solids},
year = {2024},
volume = {183},
pages = {105492},
}
@Article{zunker2024mechanicallyII,
author = {Zunker, William and Kamrin, Ken},
title = {A mechanically-derived contact model for adhesive elastic-perfectly plastic particles,
Part II: Contact under high compaction—modeling a bulk elastic response},
journal = {Journal of the Mechanics and Physics of Solids},
year = {2024},
volume = {183},
pages = {105493},
}
@Article{zunker2025experimentally,
author = {Zunker, William and Dunatunga, Sachith and Thakur, Subhash and Tang, Pingjun and Kamrin, Ken},
title = {Experimentally validated DEM for large deformation powder compaction:
mechanically-derived contact model and screening of non-physical contacts},
journal = {Powder Technology},
year = {2025},
pages = {120972},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.2
ghost atom cutoff = 3.2
binsize = 1.6, bins = 13 13 13
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/atomonly/newtoff
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 74.54 | 74.54 | 74.54 Mbytes
Dt Step Atoms KinEng c_1 Volume
1e-06 0 12 0 0 8000
Loop time of 8.28e-07 on 1 procs for 0 steps with 12 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 8.28e-07 | | |100.00
Nlocal: 12 ave 12 max 12 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: 66 ave 66 max 66 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 66
Ave neighs/atom = 5.5
Neighbor list builds = 0
Dangerous builds = 0
# print out contact area evolution for particles 1 and 12
compute Ac_1_12 particles_1_12 pair/local p13 cutoff radius
compute Ac_1_12_sum particles_1_12 reduce sum c_Ac_1_12 inputs local
variable Ac_1_12 equal c_Ac_1_12_sum
#fix logArea all print 100 "${plane_disp} ${Ac_1_12}" file pair_1_12_contact_area_triaxial12.csv screen no
variable plane_disp equal ${ddisp}*elapsed
variable plane_disp equal 1e-05*elapsed
variable plane_disp_neg equal -${ddisp}*elapsed
variable plane_disp_neg equal -1e-05*elapsed
run ${compression_steps}
run 49900
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.2
ghost atom cutoff = 3.2
binsize = 1.6, bins = 13 13 13
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair granular, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/atomonly/newtoff
stencil: full/bin/3d
bin: standard
(2) compute pair/local, occasional
attributes: half, newton off, size
pair build: half/size/bin/atomonly/newtoff
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 75.17 | 75.17 | 75.17 Mbytes
Dt Step Atoms KinEng c_1 Volume
1e-06 0 12 0 0 8000
1e-06 100 12 0.063728867 0 8000
1e-06 200 12 0.79328888 0 8000
1e-06 300 12 3.1671095 0 8000
1e-06 400 12 8.7248683 0 8000
1e-06 500 12 20.158012 0 8000
1e-06 600 12 41.157061 0 8000
1e-06 700 12 76.628872 0 8000
1e-06 800 12 132.88829 0 8000
1e-06 900 12 217.80403 0 8000
1e-06 1000 12 340.91325 0 8000
1e-06 1100 12 513.50254 0 8000
1e-06 1200 12 748.65202 0 8000
1e-06 1300 12 1061.2394 0 8000
1e-06 1400 12 1467.9017 0 8000
1e-06 1500 12 1986.9524 0 8000
1e-06 1600 12 2638.2542 0 8000
1e-06 1700 12 3443.0464 0 8000
1e-06 1800 12 4423.728 0 8000
1e-06 1900 12 5603.6004 0 8000
1e-06 2000 12 7006.5697 0 8000
1e-06 2100 12 8656.8153 0 8000
1e-06 2200 12 10575.061 0.00041930161 8000
1e-06 2300 12 12776.34 0.031472922 8000
1e-06 2400 12 15285.834 0.16547279 8000
1e-06 2500 12 18123.472 0.48824818 8000
1e-06 2600 12 21306.73 1.1172148 8000
1e-06 2700 12 24850.635 2.2101203 8000
1e-06 2800 12 28767.448 3.9742876 8000
1e-06 2900 12 33066.341 6.6765245 8000
1e-06 3000 12 37753.104 10.653677 8000
1e-06 3100 12 42829.905 16.323673 8000
1e-06 3200 12 48295.143 24.196804 8000
1e-06 3300 12 54143.784 34.886968 8000
1e-06 3400 12 60367.427 49.122473 8000
1e-06 3500 12 66954.459 67.756017 8000
1e-06 3600 12 73890.367 91.773371 8000
1e-06 3700 12 81158.051 122.30029 8000
1e-06 3800 12 88738.15 160.60714 8000
1e-06 3900 12 96609.374 208.11075 8000
1e-06 4000 12 104748.82 266.37305 8000
1e-06 4100 12 113132.27 337.09603 8000
1e-06 4200 12 121734.46 422.11267 8000
1e-06 4300 12 130529.26 523.37361 8000
1e-06 4400 12 139489.96 642.8869 8000
1e-06 4500 12 148590.48 781.76659 8000
1e-06 4600 12 157805.54 939.73777 8000
1e-06 4700 12 167102.78 1115.3765 8000
1e-06 4800 12 176408.3 1304.8823 8000
1e-06 4900 12 185727.22 1506.1791 8000
1e-06 5000 12 195037.08 1715.5141 8000
1e-06 5100 12 204311.37 1928.3496 8000
1e-06 5200 12 213522.05 2139.6607 8000
1e-06 5300 12 222640.01 2344.2078 8000
1e-06 5400 12 231635.3 2536.8271 8000
1e-06 5500 12 240477.26 2712.7272 8000
1e-06 5600 12 249036.18 2865.4067 8000
1e-06 5700 12 257225.21 2990.2307 8000
1e-06 5800 12 265107.22 3088.4777 8000
1e-06 5900 12 272662.78 3160.202 8000
1e-06 6000 12 279867.43 3206.6334 8000
1e-06 6100 12 286696.38 3230.2607 8000
1e-06 6200 12 293126.06 3234.7442 8000
1e-06 6300 12 299135.09 3224.7366 8000
1e-06 6400 12 304704.84 3205.6378 8000
1e-06 6500 12 309820.07 3183.3082 8000
1e-06 6600 12 314469.34 3163.76 8000
1e-06 6700 12 318645.43 3152.8517 8000
1e-06 6800 12 322345.74 3156.004 8000
1e-06 6900 12 325572.61 3177.9574 8000
1e-06 7000 12 328333.69 3222.5849 8000
1e-06 7100 12 330642.36 3292.7692 8000
1e-06 7200 12 332518.34 3390.3494 8000
1e-06 7300 12 333988.86 3516.133 8000
1e-06 7400 12 335091.17 3669.9688 8000
1e-06 7500 12 335881.45 3850.8676 8000
1e-06 7600 12 336541.99 4057.1561 8000
1e-06 7700 12 337100.25 4286.6487 8000
1e-06 7800 12 337436.07 4536.819 8000
1e-06 7900 12 337576.23 4804.9572 8000
1e-06 8000 12 337553.74 5088.3001 8000
1e-06 8100 12 337412.69 5384.125 8000
1e-06 8200 12 337266.12 5689.8034 8000
1e-06 8300 12 337141.16 6002.815 8000
1e-06 8400 12 336990.23 6320.7444 8000
1e-06 8500 12 336832.35 6645.3584 8000
1e-06 8600 12 336684.67 6980.6347 8000
1e-06 8700 12 336479.86 7317.4769 8000
1e-06 8800 12 336286.29 7653.1265 8000
1e-06 8900 12 336134.3 7982.859 8000
1e-06 9000 12 336043.31 8307.1796 8000
1e-06 9100 12 336035 8626.669 8000
1e-06 9200 12 336134.55 8942.2162 8000
1e-06 9300 12 336370.73 9254.9724 8000
1e-06 9400 12 336775.97 9566.1537 8000
1e-06 9500 12 337386.26 9876.5005 8000
1e-06 9600 12 338238.87 10185.038 8000
1e-06 9700 12 339373.93 10490.42 8000
1e-06 9800 12 340832.84 10792.816 8000
1e-06 9900 12 342649.99 11091.69 8000
1e-06 10000 12 344857.32 11386.232 8000
1e-06 10100 12 347498.52 11676.525 8000
1e-06 10200 12 350625.53 11966.038 8000
1e-06 10300 12 354228.27 12250.382 8000
1e-06 10400 12 358314.64 12529.915 8000
1e-06 10500 12 362887.71 12806.586 8000
1e-06 10600 12 367944.26 13083.935 8000
1e-06 10700 12 373508.47 13375.901 8000
1e-06 10800 12 379544.75 13682.748 8000
1e-06 10900 12 385955.58 13992.431 8000
1e-06 11000 12 392687 14307.793 8000
1e-06 11100 12 399676.01 14631.631 8000
1e-06 11200 12 406851.99 14966.316 8000
1e-06 11300 12 414139.37 15312.299 8000
1e-06 11400 12 421458.35 15668.76 8000
1e-06 11500 12 428725.85 16034.567 8000
1e-06 11600 12 435860.63 16408.01 8000
1e-06 11700 12 442914.03 16784.22 8000
1e-06 11800 12 449956.98 17165.7 8000
1e-06 11900 12 456943.52 17548.894 8000
1e-06 12000 12 463832.6 17927.761 8000
1e-06 12100 12 470563.99 18302.718 8000
1e-06 12200 12 477048.89 18678.218 8000
1e-06 12300 12 483212.97 19059.367 8000
1e-06 12400 12 489085.23 19458.596 8000
1e-06 12500 12 494661.19 19885.306 8000
1e-06 12600 12 499940 20344.66 8000
1e-06 12700 12 504927.83 20838.53 8000
1e-06 12800 12 509641.24 21366.554 8000
1e-06 12900 12 514117.28 21934.019 8000
1e-06 13000 12 518378.2 22538.416 8000
1e-06 13100 12 522458.77 23167.62 8000
1e-06 13200 12 525853.3 23780.032 8000
1e-06 13300 12 528815.22 24345.078 8000
1e-06 13400 12 531513.34 24883.702 8000
1e-06 13500 12 534014.75 25400.482 8000
1e-06 13600 12 536357.43 25891.923 8000
1e-06 13700 12 538572.95 26355.972 8000
1e-06 13800 12 540657.99 26795.836 8000
1e-06 13900 12 542612.1 27223.435 8000
1e-06 14000 12 544466.84 27647.413 8000
1e-06 14100 12 546241.59 28080.229 8000
1e-06 14200 12 547953.9 28538.741 8000
1e-06 14300 12 549620.46 29043.928 8000
1e-06 14400 12 551260.1 29617.65 8000
1e-06 14500 12 552886.91 30280.697 8000
1e-06 14600 12 554517.93 31050.292 8000
1e-06 14700 12 556175.17 31938.659 8000
1e-06 14800 12 557897.11 32951.814 8000
1e-06 14900 12 559696.65 34092.387 8000
1e-06 15000 12 561564.33 35360.561 8000
1e-06 15100 12 563512.54 36749.828 8000
1e-06 15200 12 565557.63 38246.838 8000
1e-06 15300 12 567718.92 39832.256 8000
1e-06 15400 12 569910.41 41477.599 8000
1e-06 15500 12 572038.38 43132.458 8000
1e-06 15600 12 573913.47 44763.446 8000
1e-06 15700 12 575651.62 46334.905 8000
1e-06 15800 12 577306.75 47812.828 8000
1e-06 15900 12 578897.86 49166.374 8000
1e-06 16000 12 580431.98 50370.863 8000
1e-06 16100 12 581917.67 51410.025 8000
1e-06 16200 12 583392.37 52290.363 8000
1e-06 16300 12 584896.54 53001.616 8000
1e-06 16400 12 586445.21 53535.481 8000
1e-06 16500 12 588052.51 53896.917 8000
1e-06 16600 12 589732.17 54102.867 8000
1e-06 16700 12 591496.83 54180.423 8000
1e-06 16800 12 593357.37 54163.728 8000
1e-06 16900 12 595249.77 54088.894 8000
1e-06 17000 12 597130.72 53987.792 8000
1e-06 17100 12 598744.15 53852.584 8000
1e-06 17200 12 600057.69 53662.064 8000
1e-06 17300 12 601263.08 53505.031 8000
1e-06 17400 12 602411.57 53452.104 8000
1e-06 17500 12 603541.22 53553.609 8000
1e-06 17600 12 604067.01 53875.668 8000
1e-06 17700 12 602571.09 54490.575 8000
1e-06 17800 12 600292.75 55434.526 8000
1e-06 17900 12 597386.86 56736.273 8000
1e-06 18000 12 593981.08 58424.745 8000
1e-06 18100 12 590178.8 60527.06 8000
1e-06 18200 12 586056.65 63073.313 8000
1e-06 18300 12 581695.18 66084.237 8000
1e-06 18400 12 577195.63 69560.379 8000
1e-06 18500 12 572657.32 73490.56 8000
1e-06 18600 12 568173.86 77853.568 8000
1e-06 18700 12 563830.46 82617.321 8000
1e-06 18800 12 559701.49 87738.316 8000
1e-06 18900 12 555848.76 93162.955 8000
1e-06 19000 12 552088.23 98803.436 8000
1e-06 19100 12 548185.32 104427.42 8000
1e-06 19200 12 544535.46 110064.18 8000
1e-06 19300 12 541228.34 115757.05 8000
1e-06 19400 12 538293.89 121467.69 8000
1e-06 19500 12 535108.7 127127.41 8000
1e-06 19600 12 531413.61 132495.98 8000
1e-06 19700 12 527729.51 137678.56 8000
1e-06 19800 12 524151.76 142754.02 8000
1e-06 19900 12 520715.23 147730.68 8000
1e-06 20000 12 517436.17 152621.73 8000
1e-06 20100 12 514316.17 157423.95 8000
1e-06 20200 12 511400.64 162074.69 8000
1e-06 20300 12 508692.38 166497.97 8000
1e-06 20400 12 506153.1 170617.84 8000
1e-06 20500 12 503717.78 174351.25 8000
1e-06 20600 12 501293.63 177615.72 8000
1e-06 20700 12 498966.36 180365.82 8000
1e-06 20800 12 496760.02 182555.39 8000
1e-06 20900 12 494705.8 184132.07 8000
1e-06 21000 12 492841.84 185052.2 8000
1e-06 21100 12 491215.97 185288.72 8000
1e-06 21200 12 489677.84 184786.05 8000
1e-06 21300 12 488104.26 183535.77 8000
1e-06 21400 12 486394.75 181560.76 8000
1e-06 21500 12 484603.38 178874.58 8000
1e-06 21600 12 482731.75 175610.89 8000
1e-06 21700 12 480707.38 172071.04 8000
1e-06 21800 12 478504.9 168244.44 8000
1e-06 21900 12 476099.5 164130.08 8000
1e-06 22000 12 473401.48 159927.13 8000
1e-06 22100 12 470370.26 155762.08 8000
1e-06 22200 12 467067.88 151634.35 8000
1e-06 22300 12 463485.76 147589.77 8000
1e-06 22400 12 459593.94 143696.49 8000
1e-06 22500 12 455376.67 140035.23 8000
1e-06 22600 12 450819.48 136692.31 8000
1e-06 22700 12 445945.91 133704.47 8000
1e-06 22800 12 440758.89 131179.35 8000
1e-06 22900 12 435302.31 129342.22 8000
1e-06 23000 12 429598.98 128282.87 8000
1e-06 23100 12 423606.11 127995.47 8000
1e-06 23200 12 417364.51 128494.32 8000
1e-06 23300 12 410931.48 129772.21 8000
1e-06 23400 12 404376.34 131791.95 8000
1e-06 23500 12 397794.05 134484.8 8000
1e-06 23600 12 390990.06 137778.07 8000
1e-06 23700 12 384162.26 141638.59 8000
1e-06 23800 12 377636.5 145932.03 8000
1e-06 23900 12 371606.04 150514.72 8000
1e-06 24000 12 366266.24 155257.47 8000
1e-06 24100 12 361786.35 160026.32 8000
1e-06 24200 12 358332.56 164701.26 8000
1e-06 24300 12 356060.82 169171.06 8000
1e-06 24400 12 355078.48 173360.16 8000
1e-06 24500 12 355450.93 177217.02 8000
1e-06 24600 12 357219.84 180708.91 8000
1e-06 24700 12 360415.01 183807.52 8000
1e-06 24800 12 365023.77 186489.43 8000
1e-06 24900 12 371003.31 188744.64 8000
1e-06 25000 12 377719.96 190508.83 8000
1e-06 25100 12 385044.02 191723.21 8000
1e-06 25200 12 392909.32 192416.99 8000
1e-06 25300 12 401135.52 192645.59 8000
1e-06 25400 12 409539.24 192477.65 8000
1e-06 25500 12 417291.42 191761.92 8000
1e-06 25600 12 424737.36 190597.14 8000
1e-06 25700 12 431913.53 189106.01 8000
1e-06 25800 12 438736.08 187391.23 8000
1e-06 25900 12 445137.75 185551.39 8000
1e-06 26000 12 451066.87 183681.98 8000
1e-06 26100 12 456506.74 181876.3 8000
1e-06 26200 12 461444.38 180210.36 8000
1e-06 26300 12 465927.86 178746.53 8000
1e-06 26400 12 470133.57 177568.71 8000
1e-06 26500 12 474134.12 176672.99 8000
1e-06 26600 12 477972.05 176033.42 8000
1e-06 26700 12 481533.44 175580.73 8000
1e-06 26800 12 484262.56 175093.24 8000
1e-06 26900 12 486070.74 174178.51 8000
1e-06 27000 12 487322.68 173184.75 8000
1e-06 27100 12 488010.07 172084.41 8000
1e-06 27200 12 488079.27 170808.69 8000
1e-06 27300 12 487463.01 169291.88 8000
1e-06 27400 12 486083.88 167484.29 8000
1e-06 27500 12 483861.52 165357.96 8000
1e-06 27600 12 480726.55 162915.35 8000
1e-06 27700 12 476628.16 160197.08 8000
1e-06 27800 12 471546.66 157277.97 8000
1e-06 27900 12 465514.41 154256.68 8000
1e-06 28000 12 458577.33 151265.67 8000
1e-06 28100 12 450810.58 148472.95 8000
1e-06 28200 12 442311.34 146058.64 8000
1e-06 28300 12 433200.29 144179.21 8000
1e-06 28400 12 423625.66 142953.04 8000
1e-06 28500 12 413765.24 142450.35 8000
1e-06 28600 12 403817.87 142689.67 8000
1e-06 28700 12 393989.03 143646.16 8000
1e-06 28800 12 384484.33 145259.76 8000
1e-06 28900 12 375502.5 147428.86 8000
1e-06 29000 12 367250.91 150041.97 8000
1e-06 29100 12 359903.16 153002.45 8000
1e-06 29200 12 353678.89 156213.09 8000
1e-06 29300 12 348513.14 159524.58 8000
1e-06 29400 12 344408.06 162793.23 8000
1e-06 29500 12 341354.25 165860.66 8000
1e-06 29600 12 339292.66 168560.48 8000
1e-06 29700 12 338131.77 170723.76 8000
1e-06 29800 12 337633.87 172131.92 8000
1e-06 29900 12 337374.11 172433.2 8000
1e-06 30000 12 337379.48 171680.35 8000
1e-06 30100 12 337530.24 169927.53 8000
1e-06 30200 12 337706.33 167168.98 8000
1e-06 30300 12 337790.98 163426.76 8000
1e-06 30400 12 337697.64 158781.65 8000
1e-06 30500 12 337366.76 153367.47 8000
1e-06 30600 12 336755.07 147361.71 8000
1e-06 30700 12 335854.47 140976.25 8000
1e-06 30800 12 334662.2 134438.92 8000
1e-06 30900 12 333206.26 127982.95 8000
1e-06 31000 12 331464.93 121911.39 8000
1e-06 31100 12 329488.62 116351.57 8000
1e-06 31200 12 327373.17 111369.57 8000
1e-06 31300 12 325228.82 107014.37 8000
1e-06 31400 12 323169.4 103330.69 8000
1e-06 31500 12 321071.03 100385.5 8000
1e-06 31600 12 319031.38 98193.648 8000
1e-06 31700 12 317126.27 96712.557 8000
1e-06 31800 12 315438.37 95876.196 8000
1e-06 31900 12 313815.51 95565.683 8000
1e-06 32000 12 312239.38 95585.612 8000
1e-06 32100 12 310926.28 95828.27 8000
1e-06 32200 12 309948.5 96173.311 8000
1e-06 32300 12 309370.35 96442.454 8000
1e-06 32400 12 309201.18 96472.304 8000
1e-06 32500 12 309383.35 96140.953 8000
1e-06 32600 12 309865.73 95349.932 8000
1e-06 32700 12 310615.88 94029.061 8000
1e-06 32800 12 311624.15 92145.895 8000
1e-06 32900 12 312897.69 89717.564 8000
1e-06 33000 12 314451.54 86812.433 8000
1e-06 33100 12 316227.53 83544.302 8000
1e-06 33200 12 318247.7 80051.39 8000
1e-06 33300 12 320540.3 76478.862 8000
1e-06 33400 12 323095.15 72955.915 8000
1e-06 33500 12 325858.6 69576.683 8000
1e-06 33600 12 328744.8 66391.967 8000
1e-06 33700 12 331653.91 63413.798 8000
1e-06 33800 12 334464.83 60630.152 8000
1e-06 33900 12 337044.79 58019.718 8000
1e-06 34000 12 339236.01 55565.231 8000
1e-06 34100 12 340903.65 53265.034 8000
1e-06 34200 12 341925.23 51135.512 8000
1e-06 34300 12 342206.93 49222.627 8000
1e-06 34400 12 341649.35 47586.207 8000
1e-06 34500 12 340176.56 46291.105 8000
1e-06 34600 12 337667.96 45393.826 8000
1e-06 34700 12 333648.9 44922.723 8000
1e-06 34800 12 328322.97 44898.764 8000
1e-06 34900 12 321776.97 45316.954 8000
1e-06 35000 12 314135.31 46151.059 8000
1e-06 35100 12 305598.53 47348.476 8000
1e-06 35200 12 296352.23 48877.862 8000
1e-06 35300 12 286690.37 50727.291 8000
1e-06 35400 12 276916.56 52890.03 8000
1e-06 35500 12 267324.34 55346.515 8000
1e-06 35600 12 258272.27 58117.818 8000
1e-06 35700 12 250043.55 61209.498 8000
1e-06 35800 12 242858.64 64607.799 8000
1e-06 35900 12 236841.89 68268.869 8000
1e-06 36000 12 232039.2 72109.967 8000
1e-06 36100 12 228474.09 76010.069 8000
1e-06 36200 12 226115.66 79808.944 8000
1e-06 36300 12 224858.91 83318.088 8000
1e-06 36400 12 224574.55 86340.123 8000
1e-06 36500 12 225062.39 88691.698 8000
1e-06 36600 12 226104.86 90211.829 8000
1e-06 36700 12 227493.83 90797.861 8000
1e-06 36800 12 229033.4 90446.128 8000
1e-06 36900 12 230503.16 89238.368 8000
1e-06 37000 12 231859.26 87294.45 8000
1e-06 37100 12 233083.51 84767.219 8000
1e-06 37200 12 234235.94 81827.155 8000
1e-06 37300 12 235402.6 78655.588 8000
1e-06 37400 12 236702.37 75432.209 8000
1e-06 37500 12 238271.62 72343.239 8000
1e-06 37600 12 240191.8 69493.919 8000
1e-06 37700 12 242533.8 66949.307 8000
1e-06 37800 12 245357.31 64751.161 8000
1e-06 37900 12 248707.62 62935.998 8000
1e-06 38000 12 252613.72 61551.838 8000
1e-06 38100 12 257052.41 60672.572 8000
1e-06 38200 12 261959.48 60392.157 8000
1e-06 38300 12 267252.31 60809.22 8000
1e-06 38400 12 272813.05 62005.004 8000
1e-06 38500 12 278498.77 64020.387 8000
1e-06 38600 12 284150.51 66835.207 8000
1e-06 38700 12 289604.09 70354.609 8000
1e-06 38800 12 294696.3 74392.688 8000
1e-06 38900 12 299233.72 78587.64 8000
1e-06 39000 12 303148.91 82674.175 8000
1e-06 39100 12 306708.36 86536.948 8000
1e-06 39200 12 309600.62 89862.067 8000
1e-06 39300 12 311700.43 92456.711 8000
1e-06 39400 12 312846.09 94218.029 8000
1e-06 39500 12 312996.55 95123.249 8000
1e-06 39600 12 311853.31 95204.167 8000
1e-06 39700 12 309573.91 94589.061 8000
1e-06 39800 12 306120.98 93445.743 8000
1e-06 39900 12 301697.58 91905.478 8000
1e-06 40000 12 296465.51 90172.857 8000
1e-06 40100 12 290548.45 88402.41 8000
1e-06 40200 12 284112.93 86721.642 8000
1e-06 40300 12 277419.21 85394.11 8000
1e-06 40400 12 270601.67 84327.103 8000
1e-06 40500 12 263782.18 83363.209 8000
1e-06 40600 12 257075.79 82350.637 8000
1e-06 40700 12 250587.81 81169.87 8000
1e-06 40800 12 244408.86 79765.108 8000
1e-06 40900 12 238613.12 78159.356 8000
1e-06 41000 12 233263.11 76444.561 8000
1e-06 41100 12 228410.45 74765.108 8000
1e-06 41200 12 224097.82 73288.059 8000
1e-06 41300 12 220360.61 72170.137 8000
1e-06 41400 12 217228.06 71527.798 8000
1e-06 41500 12 214724.04 71415.43 8000
1e-06 41600 12 212866.32 71815.969 8000
1e-06 41700 12 211661 72645.932 8000
1e-06 41800 12 211103.8 73762.785 8000
1e-06 41900 12 211177.1 74986.705 8000
1e-06 42000 12 211607.62 76028.195 8000
1e-06 42100 12 212363.62 76700.039 8000
1e-06 42200 12 213529.03 76938.547 8000
1e-06 42300 12 215008.35 76693.739 8000
1e-06 42400 12 216674.6 75984.606 8000
1e-06 42500 12 218453.89 74873.786 8000
1e-06 42600 12 220270.22 73459.542 8000
1e-06 42700 12 222044.1 71860.203 8000
1e-06 42800 12 223693.34 70197.611 8000
1e-06 42900 12 225131.14 68583.075 8000
1e-06 43000 12 226264.5 67108.382 8000
1e-06 43100 12 227001.96 65842.14 8000
1e-06 43200 12 227259.44 64830.806 8000
1e-06 43300 12 226966.5 64102.73 8000
1e-06 43400 12 226072.23 63673.107 8000
1e-06 43500 12 224550.01 63547.892 8000
1e-06 43600 12 222400.27 63725.546 8000
1e-06 43700 12 219649.08 64198.122 8000
1e-06 43800 12 216345.77 64940.248 8000
1e-06 43900 12 212561.67 65898.806 8000
1e-06 44000 12 208386.13 66994.934 8000
1e-06 44100 12 203921.52 68131.378 8000
1e-06 44200 12 199278.14 69204.386 8000
1e-06 44300 12 194569.44 70118.481 8000
1e-06 44400 12 189909.06 70810.594 8000
1e-06 44500 12 185407.95 71268.155 8000
1e-06 44600 12 181166.51 71493.826 8000
1e-06 44700 12 177276.76 71524.448 8000
1e-06 44800 12 173823.45 71423.226 8000
1e-06 44900 12 170886.41 71262.132 8000
1e-06 45000 12 168528.37 71107.616 8000
1e-06 45100 12 166817.96 70991.562 8000
1e-06 45200 12 165820.31 70920.666 8000
1e-06 45300 12 165574.99 70863.13 8000
1e-06 45400 12 166019.37 70710.029 8000
1e-06 45500 12 167147.87 70350.412 8000
1e-06 45600 12 169082.77 69657.821 8000
1e-06 45700 12 171945.43 68520.345 8000
1e-06 45800 12 175909.9 66883.643 8000
1e-06 45900 12 181195.22 64747.392 8000
1e-06 46000 12 188023.1 62178.63 8000
1e-06 46100 12 196442.27 59308.946 8000
1e-06 46200 12 206276.92 56311.64 8000
1e-06 46300 12 217187.2 53375.161 8000
1e-06 46400 12 228713.53 50677.575 8000
1e-06 46500 12 240278.4 48364.725 8000
1e-06 46600 12 251273.01 46535.827 8000
1e-06 46700 12 261407.3 45239.704 8000
1e-06 46800 12 270264.36 44479.416 8000
1e-06 46900 12 277578.87 44223.038 8000
1e-06 47000 12 283258 44417.235 8000
1e-06 47100 12 287156.44 45000.19 8000
1e-06 47200 12 289242.87 45911.176 8000
1e-06 47300 12 289597.36 47095.056 8000
1e-06 47400 12 288380.97 48501.691 8000
1e-06 47500 12 285805.13 50081.427 8000
1e-06 47600 12 282130.22 51780.572 8000
1e-06 47700 12 277128.82 53385.936 8000
1e-06 47800 12 271407.61 54873.773 8000
1e-06 47900 12 265556.17 56217.287 8000
1e-06 48000 12 260082.32 57338.782 8000
1e-06 48100 12 255399.15 58166.789 8000
1e-06 48200 12 251785.89 58653.934 8000
1e-06 48300 12 249277.86 58789.891 8000
1e-06 48400 12 247494.11 58609.44 8000
1e-06 48500 12 245660.12 58192.865 8000
1e-06 48600 12 242968.44 57656.856 8000
1e-06 48700 12 238968.69 57140.878 8000
1e-06 48800 12 233565.17 56788.953 8000
1e-06 48900 12 227411.99 56720.334 8000
1e-06 49000 12 221053.64 57003.014 8000
1e-06 49100 12 215153.96 57629.419 8000
1e-06 49200 12 210402.16 58574.859 8000
1e-06 49300 12 207216.41 59750.238 8000
1e-06 49400 12 205860.43 61020.818 8000
1e-06 49500 12 206382.26 62237.849 8000
1e-06 49600 12 208600.44 63264.958 8000
1e-06 49700 12 212280.2 63999.734 8000
1e-06 49800 12 217167.6 64388.533 8000
1e-06 49900 12 223002.61 64430.977 8000
Loop time of 0.997677 on 1 procs for 49900 steps with 12 atoms
99.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24529 | 0.24529 | 0.24529 | 0.0 | 24.59
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0019929 | 0.0019929 | 0.0019929 | 0.0 | 0.20
Output | 0.0024977 | 0.0024977 | 0.0024977 | 0.0 | 0.25
Modify | 0.74056 | 0.74056 | 0.74056 | 0.0 | 74.23
Other | | 0.007341 | | | 0.74
Nlocal: 12 ave 12 max 12 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: 66 ave 66 max 66 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 66
Ave neighs/atom = 5.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

103
examples/plugins/LAMMPSInterfaceCXX.cmake
View File

@ -33,90 +33,49 @@ endif()
################################################################################
# MPI configuration
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
find_package(MPI QUIET COMPONENTS CXX)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
option(BUILD_MPI "Build MPI version" OFF)
endif()
if(BUILD_MPI)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
# Download and configure MinGW compatible MPICH development files for Windows
option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
if(USE_MSMPI)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
else()
find_package(MPI REQUIRED)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)