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Merge pull request #3387 from akohlmey/collected-small-changes

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Collected small changes and bug fixes
This commit is contained in:
Axel Kohlmeyer
2022-08-10 18:34:52 -04:00
committed by GitHub
parent ee89ef6084 e592f0f139
commit c9c3f68bdf
12 changed files with 187 additions and 149 deletions
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19
doc/src/Run_options.rst
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@ -14,6 +14,7 @@ letter abbreviation can be used:
* :ref:`-m or -mpicolor <mpicolor>`
* :ref:`-c or -cite <cite>`
* :ref:`-nc or -nocite <nocite>`
* :ref:`-nb or -nonbuf <nonbuf>`
* :ref:`-pk or -package <package>`
* :ref:`-p or -partition <partition>`
* :ref:`-pl or -plog <plog>`
@ -257,6 +258,24 @@ Disable generating a citation reminder (see above) at all.
----------
.. _nonbuf:
**-nonbuf**
Turn off buffering for screen and logfile output. For performance
reasons, output to the screen and logfile is usually buffered, i.e.
output is only written to a file if its buffer - typically 4096 bytes -
has been filled. When LAMMPS crashes for some reason, however, that can
mean that there is important output missing. With this flag the
buffering can be turned off (only for screen and logfile output) and any
output will be committed immediately. Note that when running in
parallel with MPI, the screen output may still be buffered by the MPI
library and this cannot be changed by LAMMPS. This flag should only be
used for debugging and not for production simulations as the performance
impact can be significant, especially for large parallel runs.
----------
.. _package:
**-package style args ....**

70
examples/neb/in.neb.hop1
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@ -1,66 +1,66 @@
# 2d NEB surface simulation, hop from surface to become adatom
dimension 2
boundary p s p
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
variable u uloop 20
variable u uloop 20
# create geometry with flat surface
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
#create_box 3 box
#create_atoms 1 box
#mass * 1.0
#create_box 3 box
#create_atoms 1 box
#mass * 1.0
#write_data initial.hop1
read_data initial.hop1
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
# initial minimization to relax surface
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
timestep 0.05
timestep 0.05
# group of NEB atoms - either block or single atom ID 412
region surround block 10 18 17 20 0 0 units box
group nebatoms region surround
#group nebatoms id 412
set group nebatoms type 3
group nonneb subtract all nebatoms
region surround block 10 18 17 20 0 0 units box
group nebatoms region surround
#group nebatoms id 412
set group nebatoms type 3
group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal
fix 3 all enforce2d
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal
fix 3 all enforce2d
thermo 100
thermo 100
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance
min_style quickmin
min_style quickmin
neb 0.0 0.1 1000 1000 100 final final.hop1
neb 0.0 0.1 1000 1000 100 final final.hop1

60
examples/neb/in.neb.hop1.end
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@ -1,56 +1,56 @@
# 2d NEB surface simulation, hop from surface to become adatom
dimension 2
boundary p s p
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
variable u uloop 20
variable u uloop 20
# create geometry with flat surface
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
lattice hex 0.9
region box block 0 20 0 10 -0.25 0.25
read_data initial.hop1.end
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
timestep 0.05
timestep 0.05
# group of NEB atoms - either block or single atom ID 412
region surround block 10 18 17 20 0 0 units box
group nebatoms region surround
#group nebatoms id 412
set group nebatoms type 3
group nonneb subtract all nebatoms
region surround block 10 18 17 20 0 0 units box
group nebatoms region surround
#group nebatoms id 412
set group nebatoms type 3
group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal end first 1.0
fix 3 all enforce2d
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0 parallel ideal end first 1.0
fix 3 all enforce2d
thermo 100
thermo 100
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance
min_style quickmin
min_style quickmin
neb 0.0 0.1 1000 1000 100 final final.hop1
neb 0.0 0.1 1000 1000 100 final final.hop1

74
examples/neb/in.neb.hop2
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@ -1,68 +1,68 @@
# 2d NEB surface simulation, hop of adatom on surface
dimension 2
boundary p s p
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
atom_modify map array sort 0 0.0
variable u uloop 20
variable u uloop 20
# create geometry with adatom
lattice hex 0.9
region box block 0 20 0 11 -0.25 0.25
region box1 block 0 20 0 10 -0.25 0.25
lattice hex 0.9
region box block 0 20 0 11 -0.25 0.25
region box1 block 0 20 0 10 -0.25 0.25
#create_box 3 box
#create_atoms 1 region box1
#create_atoms 1 single 11.5 10.5 0
#mass * 1.0
#create_box 3 box
#create_atoms 1 region box1
#create_atoms 1 single 11.5 10.5 0
#mass * 1.0
#write_data initial.hop2
read_data initial.hop2
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
pair_modify shift yes
# initial minimization to relax surface
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
region 1 block INF INF INF 1.25 INF INF
group lower region 1
group mobile subtract all lower
set group lower type 2
timestep 0.05
timestep 0.05
# group of NEB atoms - either block or single atom ID 421
region surround block 10 18 17 21 0 0 units box
group nebatoms region surround
#group nebatoms id 421
set group nebatoms type 3
group nonneb subtract all nebatoms
region surround block 10 18 17 21 0 0 units box
group nebatoms region surround
#group nebatoms id 421
set group nebatoms type 3
group nonneb subtract all nebatoms
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0
fix 3 all enforce2d
fix 1 lower setforce 0.0 0.0 0.0
fix 2 nebatoms neb 1.0
fix 3 all enforce2d
thermo 100
thermo 100
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
#dump 1 nebatoms atom 10 dump.neb.$u
#dump 2 nonneb atom 10 dump.nonneb.$u
# run NEB for 2000 steps or to force tolerance
min_style fire
min_style fire
neb 0.0 0.05 1000 1000 100 final final.hop2
neb 0.0 0.05 1000 1000 100 final final.hop2

28
examples/neb/in.neb.sivac
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@ -5,7 +5,7 @@ units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
atom_modify sort 0 0.0
# coordination number cutoff
@ -45,7 +45,7 @@ group Si type 1
group del id 300
delete_atoms group del compress no
group vacneigh id 174 175 301 304 306 331 337
# choose potential
pair_style sw
@ -53,26 +53,26 @@ pair_coeff * * Si.sw Si
# set up neb run
variable u uloop 20
variable u uloop 20
# initial minimization to relax vacancy
displace_atoms all random 0.1 0.1 0.1 123456
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
# only output atoms near vacancy
#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z
# initial minimization to relax vacancy
fix 1 all neb 1.0
displace_atoms all random 0.1 0.1 0.1 123456
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
fix 1 all neb 1.0
thermo 100
thermo 100
# run NEB for 2000 steps or to force tolerance
timestep 0.01
min_style quickmin
min_style quickmin
neb 0.0 0.01 100 100 10 final final.sivac
neb 0.0 0.01 100 100 10 final final.sivac

5
src/AMOEBA/amoeba_induce.cpp
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@ -369,7 +369,8 @@ void PairAmoeba::induce()
eps = DEBYE * sqrt(eps/atom->natoms);
if (eps < poleps) done = true;
if (eps > epsold) done = true;
// also commented out in induce.f of Tinker
// if (eps > epsold) done = true;
if (iter >= politer) done = true;
// apply a "peek" iteration to the mutual induced dipoles
@ -390,7 +391,7 @@ void PairAmoeba::induce()
// terminate the calculation if dipoles failed to converge
// NOTE: could make this an error
if (iter >= maxiter || eps > epsold)
if (iter >= politer || eps > epsold)
if (comm->me == 0)
error->warning(FLERR,"AMOEBA induced dipoles did not converge");
}

20
src/KOKKOS/kokkos.cpp
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@ -116,7 +116,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
while (iarg < narg) {
if (strcmp(arg[iarg],"d") == 0 || strcmp(arg[iarg],"device") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid Kokkos command-line args");
device = atoi(arg[iarg+1]);
device = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"g") == 0 ||
@ -125,11 +125,11 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
error->all(FLERR,"GPUs are requested but Kokkos has not been compiled using a GPU-enabled backend");
#endif
if (iarg+2 > narg) error->all(FLERR,"Invalid Kokkos command-line args");
ngpus = atoi(arg[iarg+1]);
ngpus = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
int skip_gpu = 9999;
if (iarg+2 < narg && isdigit(arg[iarg+2][0])) {
skip_gpu = atoi(arg[iarg+2]);
skip_gpu = utils::inumeric(FLERR, arg[iarg+2], false, lmp);
iarg++;
}
iarg += 2;
@ -173,7 +173,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
} else if (strcmp(arg[iarg],"t") == 0 ||
strcmp(arg[iarg],"threads") == 0) {
nthreads = atoi(arg[iarg+1]);
nthreads = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
if (nthreads <= 0)
error->all(FLERR,"Invalid number of threads requested for Kokkos: must be 1 or greater");
@ -182,19 +182,20 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
} else if (strcmp(arg[iarg],"n") == 0 ||
strcmp(arg[iarg],"numa") == 0) {
numa = atoi(arg[iarg+1]);
numa = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
iarg += 2;
} else error->all(FLERR,"Invalid Kokkos command-line args");
} else error->all(FLERR,"Invalid Kokkos command-line arg: {}", arg[iarg]);
}
// Initialize Kokkos. However, we cannot change any
// Kokkos library parameters after the first initalization
if (args.num_threads != -1) {
if (args.num_threads != nthreads || args.num_numa != numa || args.device_id != device)
if ((args.num_threads != nthreads) || (args.num_numa != numa) || (args.device_id != device))
if (me == 0)
error->warning(FLERR,"Kokkos package already initalized, cannot reinitialize with different parameters");
error->warning(FLERR,"Kokkos package already initalized, "
"cannot reinitialize with different parameters");
nthreads = args.num_threads;
numa = args.num_numa;
device = args.device_id;
@ -206,8 +207,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
init_ngpus = ngpus;
}
if (me == 0)
utils::logmesg(lmp, " will use up to {} GPU(s) per node\n",ngpus);
if (me == 0) utils::logmesg(lmp, " will use up to {} GPU(s) per node\n", ngpus);
#ifdef LMP_KOKKOS_GPU
if (ngpus <= 0)

2
src/compute_pair_local.cpp
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@ -68,7 +68,7 @@ ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) :
pstyle[nvalues++] = DZ;
else if (arg[iarg][0] == 'p') {
int n = atoi(&arg[iarg][1]);
if (n <= 0) error->all(FLERR, "Invalid keyword in compute pair/local command");
if (n <= 0) error->all(FLERR, "Invalid keyword {} in compute pair/local command", arg[iarg]);
pstyle[nvalues] = PN;
pindex[nvalues++] = n - 1;

4
src/fmt/format.h
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@ -389,11 +389,11 @@ class uint128_fallback {
hi_ += (lo_ < n ? 1 : 0);
return *this;
}
#if FMT_HAS_BUILTIN(__builtin_addcll)
#if FMT_HAS_BUILTIN(__builtin_addcll) && !defined(__ibmxl__)
unsigned long long carry;
lo_ = __builtin_addcll(lo_, n, 0, &carry);
hi_ += carry;
#elif FMT_HAS_BUILTIN(__builtin_ia32_addcarryx_u64)
#elif FMT_HAS_BUILTIN(__builtin_ia32_addcarryx_u64) && !defined(__ibmxl__)
unsigned long long result;
auto carry = __builtin_ia32_addcarryx_u64(0, lo_, n, &result);
lo_ = result;

16
src/lammps.cpp
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@ -196,6 +196,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
int citelogfile = CiteMe::VERBOSE;
char *citefile = nullptr;
int helpflag = 0;
int nonbufflag = 0;
suffix = suffix2 = suffixp = nullptr;
suffix_enable = 0;
@ -298,6 +299,11 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
citeflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"-nonbuf") == 0 ||
strcmp(arg[iarg],"-nb") == 0) {
nonbufflag = 1;
iarg++;
} else if (strcmp(arg[iarg],"-package") == 0 ||
strcmp(arg[iarg],"-pk") == 0) {
if (iarg+2 > narg)
@ -520,7 +526,6 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
utils::flush_buffers(this);
}
// universe is one or more worlds, as setup by partition switch
// split universe communicator into separate world communicators
// set world screen, logfile, communicator, infile
@ -587,6 +592,15 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
}
}
// make all screen and logfile output unbuffered for debugging crashes
if (nonbufflag) {
if (universe->uscreen) setbuf(universe->uscreen, nullptr);
if (universe->ulogfile) setbuf(universe->ulogfile, nullptr);
if (screen) setbuf(screen, nullptr);
if (logfile) setbuf(logfile, nullptr);
}
// screen and logfile messages for universe and world
if ((universe->me == 0) && (!helpflag)) {

3
src/reader_xyz.cpp
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@ -179,8 +179,7 @@ void ReaderXYZ::read_atoms(int n, int nfield, double **fields)
++nid;
rv = sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz);
if (rv != 3)
error->one(FLERR,"Dump file is incorrectly formatted");
if (rv != 3) error->one(FLERR,"Dump file is incorrectly formatted");
// XXX: we could insert an element2type translation here
// XXX: for now we flag unrecognized types as type 0,

35
tools/python/pizza/dump.py
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@ -189,16 +189,26 @@ import sys, re, glob, types
from os import popen
from math import * # any function could be used by set()
try:
import numpy as np
oldnumeric = False
except:
import Numeric as np
oldnumeric = True
import numpy as np
try: from DEFAULTS import PIZZA_GUNZIP
except: PIZZA_GUNZIP = "gunzip"
# --------------------------------------------------------------------
# wrapper to convert old style comparision function to key function
def cmp2key(oldcmp):
class keycmp:
def __init__(self, obj, *args):
self.obj = obj
def __lt__(self, other):
return oldcmp(self.obj,other.obj) < 0
def __gt__(self, other):
return oldcmp(self.obj,other.obj) > 0
def __eq__(self, other):
return oldcmp(self.obj,other.obj) == 0
return keycmp
# Class definition
class dump:
@ -260,7 +270,7 @@ class dump:
# sort entries by timestep, cull duplicates
self.snaps.sort(self.compare_time)
self.snaps.sort(key=cmp2key(self.compare_time))
self.cull()
self.nsnaps = len(self.snaps)
print("read %d snapshots" % self.nsnaps)
@ -379,10 +389,7 @@ class dump:
for i in range(1,snap.natoms):
words += f.readline().decode().split()
floats = map(float,words)
if oldnumeric:
atom_data = np.array(list(floats),np.Float)
else:
atom_data = np.array(list(floats),np.float)
atom_data = np.array(list(floats),np.float)
snap.atoms = atom_data.reshape((snap.natoms, ncol))
else:
@ -858,8 +865,7 @@ class dump:
self.map(ncol+1,str)
for snap in self.snaps:
atoms = snap.atoms
if oldnumeric: newatoms = np.zeros((snap.natoms,ncol+1),np.Float)
else: newatoms = np.zeros((snap.natoms,ncol+1),np.float)
newatoms = np.zeros((snap.natoms,ncol+1),np.float)
newatoms[:,0:ncol] = snap.atoms
snap.atoms = newatoms
@ -1018,8 +1024,7 @@ class dump:
# convert values to int and absolute value since can be negative types
if oldnumeric: bondlist = np.zeros((nbonds,4),np.Int)
else: bondlist = np.zeros((nbonds,4),np.int)
bondlist = np.zeros((nbonds,4),np.int)
ints = [abs(int(value)) for value in words]
start = 0
stop = 4