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Merge branch 'master' into pair-hybrid-scaled

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This commit is contained in:
Axel Kohlmeyer
2021-04-09 22:21:16 -04:00
parent d507c57c8a 9b78426eba
commit 0628bb89ce
30 changed files with 335 additions and 347 deletions
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15
doc/src/compute_pressure.rst
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@ -46,13 +46,14 @@ system volume (or area in 2d). The second term is the virial, equal to
-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
many-body, and long-range interactions, where :math:`r_i` and
:math:`f_i` are the position and force vector of atom *i*, and the black
dot indicates a dot product. When periodic boundary conditions are
used, N' necessarily includes periodic image (ghost) atoms outside the
central box, and the position and force vectors of ghost atoms are thus
included in the summation. When periodic boundary conditions are not
used, N' = N = the number of atoms in the system. :doc:`Fixes <fix>`
that impose constraints (e.g. the :doc:`fix shake <fix_shake>` command)
also contribute to the virial term.
dot indicates a dot product. This is computed in parallel for each
sub-domain and then summed over all parallel processes. Thus N'
necessarily includes atoms from neighboring sub-domains (so-called ghost
atoms) and the position and force vectors of ghost atoms are thus
included in the summation. Only when running in serial and without
periodic boundary conditions is N' = N = the number of atoms in the
system. :doc:`Fixes <fix>` that impose constraints (e.g. the :doc:`fix
shake <fix_shake>` command) may also contribute to the virial term.
A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The 6 components of the vector are

2
examples/melt/in.melt
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@ -9,7 +9,7 @@ create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 3.0 87287
velocity all create 3.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5

85
examples/melt/log.27Nov18.melt.g++.4
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@ -1,85 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.00041604 secs
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms
Performance: 483592.231 tau/day, 1119.426 timesteps/s
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05
Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29
Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47
Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09
Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72
Other | | 0.00085 | | | 0.38
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

50
examples/melt/log.27Nov18.melt.g++.1 → examples/melt/log.8Apr21.melt.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Nov 2018)
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
@ -6,17 +6,17 @@ units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000645638 secs
create_atoms CPU = 0.002 seconds
mass 1 1.0
velocity all create 3.0 87287
velocity all create 3.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
@ -48,38 +48,38 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.222 | 3.222 | 3.222 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms
50 1.6842865 -4.8082494 0 -2.2824513 5.5666131
100 1.6712577 -4.7875609 0 -2.281301 5.6613913
150 1.6444751 -4.7471034 0 -2.2810074 5.8614211
200 1.6471542 -4.7509053 0 -2.2807916 5.8805431
250 1.6645597 -4.7774327 0 -2.2812174 5.7526089
Loop time of 1.61045 on 1 procs for 250 steps with 4000 atoms
Performance: 147983.915 tau/day, 342.555 timesteps/s
Performance: 67062.020 tau/day, 155.236 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12
Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63
Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86
Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02
Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97
Other | | 0.002878 | | | 0.39
Pair | 1.3961 | 1.3961 | 1.3961 | 0.0 | 86.69
Neigh | 0.13555 | 0.13555 | 0.13555 | 0.0 | 8.42
Comm | 0.037732 | 0.037732 | 0.037732 | 0.0 | 2.34
Output | 0.0003345 | 0.0003345 | 0.0003345 | 0.0 | 0.02
Modify | 0.038016 | 0.038016 | 0.038016 | 0.0 | 2.36
Other | | 0.002731 | | | 0.17
Nlocal: 4000 ave 4000 max 4000 min
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Nghost: 5506.00 ave 5506 max 5506 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Neighs: 151788.0 ave 151788 max 151788 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Total # of neighbors = 151788
Ave neighs/atom = 37.947000
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00
Total wall time: 0:00:01

85
examples/melt/log.8Apr21.melt.g++.4 Normal file
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@ -0,0 +1,85 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 3.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.706 | 2.706 | 2.706 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6842865 -4.8082494 0 -2.2824513 5.5666131
100 1.6712577 -4.7875609 0 -2.281301 5.6613913
150 1.6444751 -4.7471034 0 -2.2810074 5.8614211
200 1.6471542 -4.7509053 0 -2.2807916 5.8805431
250 1.6645597 -4.7774327 0 -2.2812174 5.7526089
Loop time of 0.490832 on 4 procs for 250 steps with 4000 atoms
Performance: 220034.754 tau/day, 509.340 timesteps/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.35932 | 0.37256 | 0.38746 | 1.9 | 75.90
Neigh | 0.035928 | 0.038449 | 0.042344 | 1.3 | 7.83
Comm | 0.053452 | 0.068917 | 0.08485 | 5.3 | 14.04
Output | 0.00015545 | 0.00023746 | 0.00047684 | 0.0 | 0.05
Modify | 0.0096958 | 0.0097951 | 0.0098989 | 0.1 | 2.00
Other | | 0.0008721 | | | 0.18
Nlocal: 1000.00 ave 1008 max 987 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 2711.25 ave 2728 max 2693 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 37947.0 ave 38966 max 37338 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 151788
Ave neighs/atom = 37.947000
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

2
src/GRANULAR/fix_wall_gran.cpp
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@ -1261,6 +1261,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
k_tangential = tangential_coeffs[0];
damp_tangential = tangential_coeffs[1]*damp_normal_prefactor;
Fscrit = tangential_coeffs[2] * Fncrit;
int thist0 = tangential_history_index;
int thist1 = thist0 + 1;
@ -1346,7 +1347,6 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz,
}
// rescale frictional displacements and forces if needed
Fscrit = tangential_coeffs[2] * Fncrit;
fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3);
if (fs > Fscrit) {
shrmag = sqrt(history[thist0]*history[thist0] +

10
src/MOLECULE/angle_cosine_periodic.cpp
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@ -17,17 +17,17 @@
#include "angle_cosine_periodic.h"
#include <cmath>
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;
@ -224,7 +224,7 @@ void AngleCosinePeriodic::coeff(int narg, char **arg)
double AngleCosinePeriodic::equilibrium_angle(int i)
{
return MY_PI*(1.0 - (b[i]>0)?0.0:1.0/static_cast<double>(multiplicity[i]));
return MY_PI*(1.0 - ((b[i]>0) ? 0.0 : (1.0/static_cast<double>(multiplicity[i]))));
}
/* ----------------------------------------------------------------------

15
src/RIGID/fix_rattle.cpp
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@ -17,17 +17,18 @@
#include "fix_rattle.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "domain.h"
#include "force.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
#include "modify.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

32
src/RIGID/fix_rigid.cpp
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@ -13,29 +13,29 @@
#include "fix_rigid.h"
#include <cmath>
#include <cstring>
#include "math_extra.h"
#include "math_eigen.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "domain.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "group.h"
#include "comm.h"
#include "random_mars.h"
#include "force.h"
#include "input.h"
#include "variable.h"
#include "math_const.h"
#include "memory.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "input.h"
#include "math_const.h"
#include "math_eigen.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "random_mars.h"
#include "respa.h"
#include "rigid_const.h"
#include "update.h"
#include "variable.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

24
src/RIGID/fix_rigid_nh.cpp
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@ -18,22 +18,24 @@
------------------------------------------------------------------------- */
#include "fix_rigid_nh.h"
#include <cmath>
#include <cstring>
#include "math_extra.h"
#include "atom.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "update.h"
#include "modify.h"
#include "fix_deform.h"
#include "group.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "memory.h"
#include "error.h"
#include "fix_deform.h"
#include "force.h"
#include "group.h"
#include "kspace.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "rigid_const.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

1
src/RIGID/fix_rigid_nvt_small.cpp
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@ -18,6 +18,7 @@
------------------------------------------------------------------------- */
#include "fix_rigid_nvt_small.h"
#include "error.h"
using namespace LAMMPS_NS;

33
src/RIGID/fix_shake.cpp
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@ -13,25 +13,26 @@
#include "fix_shake.h"
#include "angle.h"
#include "atom.h"
#include "atom_vec.h"
#include "bond.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_respa.h"
#include "force.h"
#include "group.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
#include "molecule.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cctype>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "domain.h"
#include "force.h"
#include "bond.h"
#include "angle.h"
#include "comm.h"
#include "group.h"
#include "fix_respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;

5
src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
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@ -581,14 +581,14 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype,
{
double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2;
double fraction,table,forcecoul,forcecoul2,forcelj;
double rrij,expn2,erfc2,expb,ecoul,evdwl,trx,tr,ftr;
double rrij,expn2,erfc2,ecoul,evdwl,trx,tr,ftr;
int itable;
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
@ -621,7 +621,6 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype,
forcecoul2 = 0.0;
prefactor2 = 0.0;
} else {
r = sqrt(rsq);
rrij = lj2[itype][jtype]*r;
expn2 = exp(-rrij*rrij);
erfc2 = erfc(rrij);

3
src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
View File

@ -586,9 +586,9 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype,
int itable;
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
@ -613,7 +613,6 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype,
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r = sqrt(rsq);
expb = lj3[itype][jtype]*exp(-lj1[itype][jtype]*r);
forcelj = expb*lj1[itype][jtype]*r;
r6inv = r2inv*r2inv*r2inv;

32
src/dump.cpp
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@ -14,16 +14,16 @@
#include "dump.h"
#include "atom.h"
#include "irregular.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "output.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "memory.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "group.h"
#include "irregular.h"
#include "memory.h"
#include "modify.h"
#include "output.h"
#include "update.h"
#include <cstring>
@ -141,12 +141,9 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
if (strchr(filename,'*')) multifile = 1;
char *suffix = filename + strlen(filename) - strlen(".bin");
if (suffix > filename && strcmp(suffix,".bin") == 0) binary = 1;
suffix = filename + strlen(filename) - strlen(".gz");
if (suffix > filename && strcmp(suffix,".gz") == 0) compressed = 1;
suffix = filename + strlen(filename) - strlen(".zst");
if (suffix > filename && strcmp(suffix,".zst") == 0) compressed = 1;
if (utils::strmatch(filename, "\\.bin$")) binary = 1;
if (utils::strmatch(filename, "\\.gz$")
|| utils::strmatch(filename, "\\.zst$")) compressed = 1;
}
/* ---------------------------------------------------------------------- */
@ -582,12 +579,11 @@ void Dump::openfile()
if (filewriter) {
if (compressed) {
#ifdef LAMMPS_GZIP
char gzip[128];
sprintf(gzip,"gzip -6 > %s",filecurrent);
auto gzip = fmt::format("gzip -6 > {}",filecurrent);
#ifdef _WIN32
fp = _popen(gzip,"wb");
fp = _popen(gzip.c_str(),"wb");
#else
fp = popen(gzip,"w");
fp = popen(gzip.c_str(),"w");
#endif
#else
error->one(FLERR,"Cannot open gzipped file");

2
src/finish.cpp
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@ -401,7 +401,7 @@ void Finish::end(int flag)
}
#endif
if (lmp->kokkos && lmp->kokkos->ngpus > 0)
if ((comm->me == 0) && lmp->kokkos && (lmp->kokkos->ngpus > 0))
if (const char* env_clb = getenv("CUDA_LAUNCH_BLOCKING"))
if (!(strcmp(env_clb,"1") == 0)) {
error->warning(FLERR,"Timing breakdown may not be accurate "

49
src/fix_tmd.cpp
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@ -18,19 +18,18 @@
#include "fix_tmd.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "memory.h"
#include "modify.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "domain.h"
#include "group.h"
#include "respa.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -520,31 +519,29 @@ void FixTMD::readfile(char *file)
void FixTMD::open(char *file)
{
compressed = 0;
char *suffix = file + strlen(file) - 3;
if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1;
if (!compressed) fp = fopen(file,"r");
else {
if (utils::strmatch(file,"\\.gz$")) {
compressed = 1;
#ifdef LAMMPS_GZIP
char gunzip[128];
snprintf(gunzip,128,"gzip -c -d %s",file);
auto gunzip = fmt::format("gzip -c -d {}",file);
#ifdef _WIN32
fp = _popen(gunzip,"rb");
fp = _popen(gunzip.c_str(),"rb");
#else
fp = popen(gunzip,"r");
fp = popen(gunzip.c_str(),"r");
#endif
#else
error->one(FLERR,"Cannot open gzipped file");
error->one(FLERR,"Cannot open gzipped file without gzip support");
#endif
} else {
compressed = 0;
fp = fopen(file,"r");
}
if (fp == nullptr) {
char str[128];
snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
if (fp == nullptr)
error->one(FLERR,fmt::format("Cannot open file {}: {}",
file, utils::getsyserror()));
}
/* ---------------------------------------------------------------------- */

13
src/input.cpp
View File

@ -1250,9 +1250,18 @@ void Input::shell()
for (int i = 1; i < narg; i++) {
rv = 0;
#ifdef _WIN32
if (arg[i]) rv = _putenv(arg[i]);
if (arg[i]) rv = _putenv(utils::strdup(arg[i]));
#else
if (arg[i]) rv = putenv(arg[i]);
if (arg[i]) {
std::string vardef(arg[i]);
auto found = vardef.find_first_of("=");
if (found == std::string::npos) {
rv = setenv(vardef.c_str(),"",1);
} else {
rv = setenv(vardef.substr(0,found).c_str(),
vardef.substr(found+1).c_str(),1);
}
}
#endif
rv = (rv < 0) ? errno : 0;
MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world);

15
src/library.cpp
View File

@ -4734,19 +4734,14 @@ void lammps_set_fix_external_callback(void *handle, char *id, FixExternalFnPtr c
BEGIN_CAPTURE
{
int ifix = lmp->modify->find_fix(id);
if (ifix < 0) {
char str[128];
snprintf(str, 128, "Can not find fix with ID '%s'!", id);
lmp->error->all(FLERR,str);
}
if (ifix < 0)
lmp->error->all(FLERR,fmt::format("Cannot find fix with ID '{}'!", id));
Fix *fix = lmp->modify->fix[ifix];
if (strcmp("external",fix->style) != 0) {
char str[128];
snprintf(str, 128, "Fix '%s' is not of style external!", id);
lmp->error->all(FLERR,str);
}
if (strcmp("external",fix->style) != 0)
lmp->error->all(FLERR,fmt::format("Fix '{}' is not of style "
"external!", id));
FixExternal * fext = (FixExternal*) fix;
fext->set_callback(callback, caller);

1
src/pair.cpp
View File

@ -204,7 +204,6 @@ void Pair::modify_params(int narg, char **arg)
else error->all(FLERR,"Illegal pair_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"nofdotr") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
no_virial_fdotr_compute = 1;
++iarg;
} else error->all(FLERR,"Illegal pair_modify command");

7
src/pair_hybrid.cpp
View File

@ -468,10 +468,7 @@ void PairHybrid::coeff(int narg, char **arg)
if (multiple[m]) {
multflag = 1;
if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients");
if (!isdigit(arg[3][0]))
error->all(FLERR,"Incorrect args for pair coefficients");
int index = utils::inumeric(FLERR,arg[3],false,lmp);
if (index == multiple[m]) break;
if (multiple[m] == utils::inumeric(FLERR,arg[3],false,lmp)) break;
else continue;
} else break;
}
@ -492,7 +489,7 @@ void PairHybrid::coeff(int narg, char **arg)
// invoke sub-style coeff() starting with 1st remaining arg
if (!none) styles[m]->coeff(narg-1-multflag,&arg[1+multflag]);
if (!none) styles[m]->coeff(narg-1-multflag,arg+1+multflag);
// if sub-style only allows one pair coeff call (with * * and type mapping)
// then unset setflag/map assigned to that style before setting it below

8
src/pair_hybrid_overlay.cpp
View File

@ -17,7 +17,6 @@
#include "error.h"
#include <cstring>
#include <cctype>
using namespace LAMMPS_NS;
@ -51,10 +50,7 @@ void PairHybridOverlay::coeff(int narg, char **arg)
if (multiple[m]) {
multflag = 1;
if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients");
if (!isdigit(arg[3][0]))
error->all(FLERR,"Incorrect args for pair coefficients");
int index = utils::inumeric(FLERR,arg[3],false,lmp);
if (index == multiple[m]) break;
if (multiple[m] == utils::inumeric(FLERR,arg[3],false,lmp)) break;
else continue;
} else break;
}
@ -75,7 +71,7 @@ void PairHybridOverlay::coeff(int narg, char **arg)
// invoke sub-style coeff() starting with 1st remaining arg
if (!none) styles[m]->coeff(narg-1-multflag,&arg[1+multflag]);
if (!none) styles[m]->coeff(narg-1-multflag,arg+1+multflag);
// set setflag and which type pairs map to which sub-style
// if sub-style is none: set hybrid subflag, wipe out map

16
src/read_data.cpp
View File

@ -1954,13 +1954,12 @@ int ReadData::reallocate(int **pcount, int cmax, int amax)
void ReadData::open(char *file)
{
compressed = 0;
char *suffix = file + strlen(file) - 3;
if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1;
if (!compressed) fp = fopen(file,"r");
else {
if (utils::strmatch(file,"\\.gz$")) {
compressed = 1;
#ifdef LAMMPS_GZIP
std::string gunzip = fmt::format("gzip -c -d {}",file);
auto gunzip = fmt::format("gzip -c -d {}",file);
#ifdef _WIN32
fp = _popen(gunzip.c_str(),"rb");
#else
@ -1968,8 +1967,11 @@ void ReadData::open(char *file)
#endif
#else
error->one(FLERR,"Cannot open gzipped file: " + utils::getsyserror());
error->one(FLERR,"Cannot open gzipped file without gzip support");
#endif
} else {
compressed = 0;
fp = fopen(file,"r");
}
if (fp == nullptr)

16
src/reader.cpp
View File

@ -37,13 +37,12 @@ void Reader::open_file(const char *file)
{
if (fp != nullptr) close_file();
compressed = 0;
const char *suffix = file + strlen(file) - 3;
if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1;
if (!compressed) fp = fopen(file,"r");
else {
if (utils::strmatch(file,"\\.gz$")) {
compressed = 1;
#ifdef LAMMPS_GZIP
std::string gunzip = fmt::format("gzip -c -d {}",file);
auto gunzip = fmt::format("gzip -c -d {}",file);
#ifdef _WIN32
fp = _popen(gunzip.c_str(),"rb");
#else
@ -51,8 +50,11 @@ void Reader::open_file(const char *file)
#endif
#else
error->one(FLERR,"Cannot open gzipped file: " + utils::getsyserror());
error->one(FLERR,"Cannot open gzipped file without gzip support");
#endif
} else {
compressed = 0;
fp = fopen(file,"r");
}
if (fp == nullptr)

11
src/variable.cpp
View File

@ -337,11 +337,11 @@ void Variable::set(int narg, char **arg)
}
if (nvar == maxvar) grow();
style[nvar] = GETENV;
num[nvar] = 1;
num[nvar] = 2;
which[nvar] = 0;
pad[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(1,&arg[2],data[nvar]);
data[nvar][0] = utils::strdup(arg[2]);
data[nvar][1] = utils::strdup("(undefined)");
// SCALARFILE for strings or numbers
@ -1252,7 +1252,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
print_var_error(FLERR,"Invalid syntax in variable formula",ivar);
expect = OP;
char *contents;
char *contents = nullptr;
i = find_matching_paren(str,i,contents,ivar);
i++;
@ -2068,7 +2068,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
// ----------------
if (str[i] == '(') {
char *contents;
char *contents = nullptr;
i = find_matching_paren(str,i,contents,ivar);
i++;
@ -3286,6 +3286,7 @@ int Variable::find_matching_paren(char *str, int i, char *&contents, int ivar)
int istop = i;
int n = istop - istart - 1;
delete[] contents;
contents = new char[n+1];
strncpy(contents,&str[istart+1],n);
contents[n] = '\0';
@ -4827,7 +4828,7 @@ double Variable::evaluate_boolean(char *str)
error->all(FLERR,"Invalid Boolean syntax in if command");
expect = OP;
char *contents;
char *contents = nullptr;
i = find_matching_paren(str,i,contents,-1);
i++;

23
unittest/commands/test_simple_commands.cpp
View File

@ -20,8 +20,8 @@
#include "output.h"
#include "update.h"
#include "utils.h"
#include "variable.h"
#include "fmt/format.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include "../testing/core.h"
@ -400,23 +400,26 @@ TEST_F(SimpleCommandsTest, Shell)
command("shell putenv TEST_VARIABLE=simpletest");
END_HIDE_OUTPUT();
char *test_var = getenv("TEST_VARIABLE");
const char *test_var = getenv("TEST_VARIABLE");
ASSERT_NE(test_var, nullptr);
ASSERT_THAT(test_var, StrEq("simpletest"));
BEGIN_HIDE_OUTPUT();
command("shell putenv TEST_VARIABLE=simpletest");
command("shell putenv TEST_VARIABLE2=simpletest2 OTHER_VARIABLE=2");
command("shell putenv TEST_VARIABLE");
command("shell putenv TEST_VARIABLE2=simpletest OTHER_VARIABLE=2");
END_HIDE_OUTPUT();
char *test_var2 = getenv("TEST_VARIABLE2");
char *other_var = getenv("OTHER_VARIABLE");
test_var = getenv("TEST_VARIABLE2");
ASSERT_NE(test_var, nullptr);
ASSERT_THAT(test_var, StrEq("simpletest"));
ASSERT_NE(test_var2, nullptr);
ASSERT_THAT(test_var2, StrEq("simpletest2"));
test_var = getenv("OTHER_VARIABLE");
ASSERT_NE(test_var, nullptr);
ASSERT_THAT(test_var, StrEq("2"));
ASSERT_NE(other_var, nullptr);
ASSERT_THAT(other_var, StrEq("2"));
test_var = getenv("TEST_VARIABLE");
ASSERT_NE(test_var, nullptr);
ASSERT_THAT(test_var, StrEq(""));
}
TEST_F(SimpleCommandsTest, CiteMe)

14
unittest/commands/test_variables.cpp
View File

@ -122,6 +122,8 @@ TEST_F(VariableTest, CreateDelete)
file_vars();
ASSERT_EQ(variable->nvar, 1);
BEGIN_HIDE_OUTPUT();
command("shell putenv TEST_VARIABLE=simpletest2");
command("shell putenv TEST_VARIABLE2=simpletest OTHER_VARIABLE=2");
command("variable one index 1 2 3 4");
command("variable two equal 1");
command("variable two equal 2");
@ -133,8 +135,8 @@ TEST_F(VariableTest, CreateDelete)
command("variable five2 loop 10 200 pad");
command("variable six world one");
command("variable seven format two \"%5.2f\"");
command("variable eight getenv PWD");
command("variable eight getenv XXXXX");
command("variable eight getenv TEST_VARIABLE2");
command("variable eight getenv XXX");
command("variable nine file test_variable.file");
command("variable ten internal 1.0");
command("variable ten internal 10.0");
@ -167,6 +169,14 @@ TEST_F(VariableTest, CreateDelete)
unlink("MYFILE");
ASSERT_THAT(variable->retrieve("file"), StrEq("0"));
BEGIN_HIDE_OUTPUT();
command("variable seven delete");
command("variable seven getenv TEST_VARIABLE");
command("variable eight getenv OTHER_VARIABLE");
END_HIDE_OUTPUT();
ASSERT_THAT(variable->retrieve("seven"), StrEq("simpletest2"));
ASSERT_THAT(variable->retrieve("eight"), StrEq("2"));
ASSERT_EQ(variable->equalstyle(variable->find("one")), 0);
ASSERT_EQ(variable->equalstyle(variable->find("two")), 1);
ASSERT_EQ(variable->equalstyle(variable->find("ten")), 1);

80
unittest/force-styles/tests/angle-cosine_periodic.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 10 Mar 2021
date_generated: Tue Apr 6 18:38:56 2021
lammps_version: 8 Apr 2021
date_generated: Thu Apr 8 09:28:11 2021
epsilon: 2.5e-13
prerequisites: ! |
atom full
@ -11,32 +11,32 @@ input_file: in.fourmol
angle_style: cosine/periodic
angle_coeff: ! |
1 75.0 1 2
2 45.0 1 2
2 45.0 -1 2
3 50.0 -1 3
4 100.0 -1 4
equilibrium: 4 1.5707963267948966 1.5707963267948966 0 0
equilibrium: 4 3.141592653589793 1.5707963267948966 2.0943951023931957 2.356194490192345
extract: ! ""
natoms: 29
init_energy: 946.676664091363
init_stress: ! |2-
3.8581448829084906e+00 -6.3926599144452858e+01 6.0068454261544439e+01 1.4347370855129017e+02 1.0109551149053127e+02 4.9470344115369670e+01
init_energy: 605.3643061001458
init_stress: ! |-
-1.7082420754402889e+01 -7.3281097507808681e+00 2.4410530505183818e+01 8.5827033671406951e+01 1.4260977966148616e+02 4.1579557432232576e+01
init_forces: ! |2
1 7.9609486050127529e+00 -3.9274211736421961e+01 -3.8917410871887981e+01
2 4.6997439470662350e+00 3.8052682089524090e+01 3.0599010994189470e+01
3 -4.4330179925982058e+01 -1.6514501437366098e+00 1.9894582317318523e+01
4 1.1465928779203908e+01 -7.1462736556935234e+00 -1.8983545733370338e+01
5 2.7634466780141157e+01 1.5504150132065057e+01 1.0078115065618357e+01
6 2.2512674572611367e+01 -5.4260358088923418e+01 -6.0646506351853276e+01
3 -7.1532072701475698e+01 9.6873528247272844e+01 7.3410935137796983e+01
4 3.1784763224659116e+01 -4.4133218046130608e+01 -6.2234613362865147e+01
5 5.8817481848549889e+01 -2.5112568523390145e+01 3.9611729278121981e+00
6 -8.7258065964885336e+00 -4.2663580774228997e+01 -1.6819642012415606e+01
7 -1.5578858996464229e+01 1.3895348629116569e+01 -3.3939856789628062e+00
8 -2.6028225001107934e+00 4.7418887884887312e+01 1.2659217319984802e+02
9 9.4419020144376677e+00 -1.3812152922900303e+01 1.2280697239365450e+00
10 3.7181742871134183e+01 -2.6592777970320334e+01 -1.0034832175946605e+02
11 1.1888648487599809e+01 -1.7288532453781471e+00 -1.8714004234488471e+00
12 1.3452345752647041e+01 3.9195153629390539e+01 -3.9429673136141247e+01
13 -4.6656310032990458e+00 -1.2502935413462930e+01 1.4918864440944628e+01
14 -2.1383527724886850e+01 -9.3422692044635554e+00 7.5125645645164223e+00
15 -8.0644375221897171e+00 -2.6783296801963008e+00 6.9267625241565547e+00
16 -7.0395776185793807e+01 4.3227686209287491e+01 3.0567216126495769e+01
8 -1.6678237064738614e+01 -2.6557373913973738e+01 8.7708427797183326e+00
9 -9.4419020144376677e+00 1.3812152922900303e+01 -1.2280697239365450e+00
10 1.0844630504236606e+02 1.9274264686364820e+01 1.2594098114786526e+01
11 -1.1888648487599809e+01 1.7288532453781471e+00 1.8714004234488471e+00
12 9.7432958614920665e+01 1.1284647087939499e+02 -1.3445218835244805e+02
13 -2.2887258478933525e+01 -5.9815335453575649e+01 4.1237962971772127e+01
14 -4.6498844054867675e+01 -3.0251289808967520e+01 1.5556535565006259e+01
15 -5.3477741242848616e+01 -1.7885978453267143e+01 4.6284681424489207e+01
16 -7.3215663693592745e+01 1.7514552522777997e+01 7.4857846653898914e+00
17 2.0782832048872386e+01 -2.8304296512773977e+01 1.5273484998106287e+01
18 1.6481336531704756e+00 1.7222946144801426e+01 -6.9896289164966490e+01
19 -2.0180190840279820e+01 -2.5140421523544326e+01 2.9933594625645306e+01
@ -50,27 +50,27 @@ init_forces: ! |2
27 -8.7971258084923178e+00 7.2217511410368814e+01 -2.4599681382405976e+01
28 -1.9235439225569891e+01 -4.3179911322776611e+01 1.0030656861974458e+00
29 2.8032565034062209e+01 -2.9037600087592210e+01 2.3596615696208531e+01
run_energy: 945.667120914027
run_stress: ! |2-
4.9007195370705645e+00 -6.4584848054201885e+01 5.9684128517131313e+01 1.4440631784196160e+02 1.0147779649040916e+02 5.0605123164347972e+01
run_energy: 603.8182365368202
run_stress: ! |-
-1.6098625319219664e+01 -7.7961962067566510e+00 2.3894821525976329e+01 8.7036156470651477e+01 1.4262918929621054e+02 4.2523803236880880e+01
run_forces: ! |2
1 8.0595707378962782e+00 -3.9275884216073550e+01 -3.8921834622274609e+01
2 4.6450877231394490e+00 3.7989319504376653e+01 3.0709930231636147e+01
3 -4.4174062041610540e+01 -1.3116774304574319e+00 1.9852389406583850e+01
4 1.1432955350908090e+01 -7.3978491536336328e+00 -1.8963452260213845e+01
5 2.7565769765719310e+01 1.5533965769082254e+01 1.0064393083030197e+01
6 2.2437947870916961e+01 -5.4321180615060769e+01 -6.0748488446866872e+01
7 -1.5585343433722571e+01 1.3904433399215314e+01 -3.4020204287915634e+00
8 -2.7173598979194153e+00 4.7428178462168347e+01 1.2654691883960646e+02
9 9.4915406599908749e+00 -1.3885257714808199e+01 1.2160209239091246e+00
10 3.7036130179485966e+01 -2.6384482125884212e+01 -1.0013051660330657e+02
11 1.1913327728618880e+01 -1.7105485662994653e+00 -1.8898750666441195e+00
12 1.3449580650332301e+01 3.9344535800585398e+01 -3.9552691785632291e+01
13 -4.6002052262583266e+00 -1.2370495939576998e+01 1.4765847794019894e+01
14 -2.1313398317698834e+01 -9.6666833306404527e+00 7.4826992840481967e+00
15 -8.0459573339780484e+00 -2.8098768831377434e+00 7.2021609989661499e+00
16 -7.0394187900784956e+01 4.3284348202675552e+01 3.0478355256814506e+01
17 2.0798603484964556e+01 -2.8350845162531051e+01 1.5290163395115368e+01
1 8.1036664069391833e+00 -3.9279459516104339e+01 -3.8959949625007155e+01
2 4.6488532958171156e+00 3.7987813821226069e+01 3.0712083303318757e+01
3 -7.1419656269516480e+01 9.7015207052323333e+01 7.3123837986656483e+01
4 3.1774739774255771e+01 -4.4324760214341296e+01 -6.1918121921961003e+01
5 5.8630133295649813e+01 -2.5003101567718115e+01 3.8957656941403842e+00
6 -8.6686835699933500e+00 -4.2717543793109854e+01 -1.6944132920021204e+01
7 -1.5605967450730276e+01 1.3924972058096937e+01 -3.4081311693274161e+00
8 -1.6735469954990947e+01 -2.6654949908594496e+01 8.9412902423392993e+00
9 -9.4705763934675620e+00 1.3861186924074314e+01 -1.2218212802251793e+00
10 1.0864309846473817e+02 1.9311615651482960e+01 1.2534898619395602e+01
11 -1.1889594908454491e+01 1.6849924892427488e+00 1.9039966312260486e+00
12 9.6643785665770423e+01 1.1329932305772147e+02 -1.3435213826206018e+02
13 -2.2815824864999897e+01 -5.9701629573330088e+01 4.1148977584672039e+01
14 -4.6226658006998740e+01 -3.0469540424436548e+01 1.5534272011399247e+01
15 -5.3141801628038777e+01 -1.8156497866651446e+01 4.6272398149175629e+01
16 -7.3254211788300807e+01 1.7569251761827239e+01 7.4522974142679850e+00
17 2.0784167932320894e+01 -2.8346879951708846e+01 1.5284477542010659e+01
18 1.7456021018344252e+00 1.7528557172698406e+01 -7.0852460721917453e+01
19 -2.0389936120749365e+01 -2.5462340563923114e+01 3.0421727677614534e+01
20 1.8644334018914940e+01 7.9337833912247095e+00 4.0430733044302912e+01

31
unittest/force-styles/yaml_writer.cpp
View File

@ -13,6 +13,7 @@
#include "yaml_writer.h"
#include "yaml.h"
#include "fmt/format.h"
#include <cstdio>
#include <string>
@ -51,41 +52,17 @@ YamlWriter::~YamlWriter()
void YamlWriter::emit(const std::string &key, const double value)
{
yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG,
(yaml_char_t *)key.c_str(), key.size(), 1, 0,
YAML_PLAIN_SCALAR_STYLE);
yaml_emitter_emit(&emitter, &event);
char buf[256];
snprintf(buf, 256, "%.15g", value);
yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG, (yaml_char_t *)buf,
strlen(buf), 1, 0, YAML_PLAIN_SCALAR_STYLE);
yaml_emitter_emit(&emitter, &event);
emit(key,fmt::format("{}",value));
}
void YamlWriter::emit(const std::string &key, const long value)
{
yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG,
(yaml_char_t *)key.c_str(), key.size(), 1, 0,
YAML_PLAIN_SCALAR_STYLE);
yaml_emitter_emit(&emitter, &event);
char buf[256];
snprintf(buf, 256, "%ld", value);
yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG, (yaml_char_t *)buf,
strlen(buf), 1, 0, YAML_PLAIN_SCALAR_STYLE);
yaml_emitter_emit(&emitter, &event);
emit(key,fmt::format("{}",value));
}
void YamlWriter::emit(const std::string &key, const int value)
{
yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG,
(yaml_char_t *)key.c_str(), key.size(), 1, 0,
YAML_PLAIN_SCALAR_STYLE);
yaml_emitter_emit(&emitter, &event);
char buf[256];
snprintf(buf, 256, "%d", value);
yaml_scalar_event_initialize(&event, NULL, (yaml_char_t *)YAML_STR_TAG, (yaml_char_t *)buf,
strlen(buf), 1, 0, YAML_PLAIN_SCALAR_STYLE);
yaml_emitter_emit(&emitter, &event);
emit(key,fmt::format("{}",value));
}
void YamlWriter::emit(const std::string &key, const std::string &value)

2
unittest/python/python-formats.py
View File

@ -4,7 +4,7 @@ from lammps.formats import LogFile, AvgChunkFile
EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples'))
DEFAULT_STYLE_EXAMPLE_LOG="melt/log.27Nov18.melt.g++.1"
DEFAULT_STYLE_EXAMPLE_LOG="melt/log.8Apr21.melt.g++.1"
MULTI_STYLE_EXAMPLE_LOG="peptide/log.27Nov18.peptide.g++.1"
AVG_CHUNK_FILE="VISCOSITY/profile.13Oct16.nemd.2d.g++.1"