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Merge branch 'snap-inner-mod' of github.com:athomps/lammps into snap-inner-mod

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This commit is contained in:
Aidan Thompson
2022-04-27 10:58:43 -06:00
parent a3c6baad4c 0e1f9968c1
commit cdba0da780
18 changed files with 674 additions and 83 deletions
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5
doc/src/compute_viscosity_cos.rst
View File

@ -21,12 +21,13 @@ Examples
.. code-block:: LAMMPS
units real
compute cos all viscosity/cos
variable V equal c_cos[7]
variable A equal 0.02E-5
variable A equal 0.02E-5 # A/fs^2
variable density equal density
variable lz equal lz
variable reciprocalViscosity equal v_V/${A}/v_density*39.4784/v_lz/v_lz*100
variable reciprocalViscosity equal v_V/${A}/v_density*39.4784/v_lz/v_lz*100 # 1/(Pa*s)
Description
"""""""""""

2
doc/src/fix_accelerate_cos.rst
View File

@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* accelerate/cos = style name of this fix command
* value = amplitude of acceleration (in unit of force/mass)
* value = amplitude of acceleration (in unit of velocity/time)
Examples

33
doc/src/fix_ave_correlate.rst
View File

@ -25,7 +25,7 @@ Syntax
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
v_name = global value calculated by an equal-style variable with name
v_name[I] = Ith component of a vector-style variable with name
v_name[I] = Ith component of a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *type* or *ave* or *start* or *prefactor* or *file* or *overwrite* or *title1* or *title2* or *title3*
@ -105,20 +105,21 @@ individual fixes for info on which ones produce such values.
ones that can be used with this fix. Variables of style *atom* cannot
be used, since they produce per-atom values.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "n\*" or
"m\*n". If N = the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).
----------
For input values from a compute or fix or variable , the bracketed
index I can be specified using a wildcard asterisk with the index to
effectively specify multiple values. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the size of the vector, then an
asterisk with no numeric values means all indices from 1 to N. A
leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to N (inclusive). A middle
asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the
vector had been listed one by one. E.g. these 2 fix ave/correlate
commands are equivalent, since the :doc:`compute pressure <compute_pressure>` command creates a global vector with 6
values.
commands are equivalent, since the :doc:`compute pressure
<compute_pressure>` command creates a global vector with 6 values.
.. code-block:: LAMMPS
@ -128,6 +129,14 @@ values.
c_myPress[1] c_myPress[2] c_myPress[3] &
c_myPress[4] c_myPress[5] c_myPress[6]
.. note::
For a vector-style variable, only the wildcard forms "\*n" or
"m\*n" are allowed. You must specify the upper bound, because
vector-style variable lengths are not determined until the variable
is evaluated. If n is specified larger than the vector length
turns out to be, zeroes are output for missing vector values.
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what

55
doc/src/fix_ave_histo.rst
View File

@ -32,7 +32,7 @@ Syntax
f_ID = scalar or vector calculated by a fix with ID
f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
v_name[I] = value calculated by a vector-style variable with name
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
@ -120,27 +120,6 @@ If *mode* = vector, then the input values must be vectors, or arrays
with a bracketed term appended, indicating the Ith column of the array
is used.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "n\*" or
"m\*n". If N = the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the
vector or columns of the array had been listed one by one. E.g. these
2 fix ave/histo commands are equivalent, since the :doc:`compute com/chunk <compute_com_chunk>` command creates a global array with
3 columns:
.. code-block:: LAMMPS
compute myCOM all com/chunk
fix 1 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[*] file tmp1.com mode vector
fix 2 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
If the fix ave/histo/weight command is used, exactly two values must
be specified. If the values are vectors, they must be the same
length. The first value (a scalar or vector) is what is histogrammed
@ -153,6 +132,38 @@ the first vector.
----------
For input values from a compute or fix or variable, the bracketed
index I can be specified using a wildcard asterisk with the index to
effectively specify multiple values. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* =
scalar) or the number of columns in the array (for *mode* = vector),
then an asterisk with no numeric values means all indices from 1 to N.
A leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to N (inclusive). A middle
asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the
vector or columns of the array had been listed one by one. E.g. these
2 fix ave/histo commands are equivalent, since the :doc:`compute
com/chunk <compute_com_chunk>` command creates a global array with 3
columns:
.. code-block:: LAMMPS
compute myCOM all com/chunk
fix 1 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[*] file tmp1.com mode vector
fix 2 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
.. note::
For a vector-style variable, only the wildcard forms "\*n" or
"m\*n" are allowed. You must specify the upper bound, because
vector-style variable lengths are not determined until the variable
is evaluated. If n is specified larger than the vector length
turns out to be, zeroes are output for missing vector values.
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
timesteps the input values will be used in order to contribute to the
histogram. The final histogram is generated on timesteps that are

44
doc/src/fix_ave_time.rst
View File

@ -25,7 +25,7 @@ Syntax
f_ID = global scalar or vector calculated by a fix with ID
f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
v_name = value(s) calculated by an equal-style or vector-style variable with name
v_name[I] = value calculated by a vector-style variable with name
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *title1* or *title2* or *title3*
@ -113,20 +113,23 @@ with a bracketed term appended, indicating the Ith column of the array
is used. All vectors must be the same length, which is the length of
the vector or number of rows in the array.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "n\*" or
"m\*n". If N = the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).
----------
For input values from a compute or fix or variable, the bracketed
index I can be specified using a wildcard asterisk with the index to
effectively specify multiple values. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* =
scalar) or the number of columns in the array (for *mode* = vector),
then an asterisk with no numeric values means all indices from 1 to N.
A leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to N (inclusive). A middle
asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the
vector or columns of the array had been listed one by one. E.g. these
2 fix ave/time commands are equivalent, since the :doc:`compute rdf <compute_rdf>` command creates, in this case, a global array
with 3 columns, each of length 50:
2 fix ave/time commands are equivalent, since the :doc:`compute rdf
<compute_rdf>` command creates, in this case, a global array with 3
columns, each of length 50:
.. code-block:: LAMMPS
@ -134,6 +137,14 @@ with 3 columns, each of length 50:
fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
.. note::
For a vector-style variable, only the wildcard forms "\*n" or
"m\*n" are allowed. You must specify the upper bound, because
vector-style variable lengths are not determined until the variable
is evaluated. If n is specified larger than the vector length
turns out to be, zeroes are output for missing vector values.
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
@ -169,9 +180,12 @@ asterisk to effectively specify multiple values.
Note that there is a :doc:`compute reduce <compute_reduce>` command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/time. Or it can be a compute defined
not in your input script, but by :doc:`thermodynamic output <thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale <fix_temp_rescale>`. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
not in your input script, but by :doc:`thermodynamic output
<thermo_style>` or other fixes such as :doc:`fix nvt <fix_nh>` or
:doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS
<Modify>`.
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If *mode* = scalar, then if

30
doc/src/thermo_style.rst
View File

@ -85,7 +85,7 @@ Syntax
f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
f_ID[I][J] = I,J component of global array calculated by a fix with ID
v_name = value calculated by an equal-style variable with name
v_name[I] = value calculated by a vector-style variable with name
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
Examples
""""""""
@ -348,16 +348,15 @@ dimensions *lx*, *ly*, *lz*, *yz*, *xz*, *xy*\ .
----------
For output values from a compute or fix, the bracketed index I used to
index a vector, as in *c_ID[I]* or *f_ID[I]*, can be specified
using a wildcard asterisk with the index to effectively specify
multiple values. This takes the form "\*" or "\*n" or "n\*" or "m\*n".
If N = the size of the vector (for *mode* = scalar) or the number of
columns in the array (for *mode* = vector), then an asterisk with no
numeric values means all indices from 1 to N. A leading asterisk
means all indices from 1 to n (inclusive). A trailing asterisk means
all indices from n to N (inclusive). A middle asterisk means all
indices from m to n (inclusive).
For output values from a compute or fix or variable, the bracketed
index I used to index a vector, as in *c_ID[I]* or *f_ID[I]* or
*v_name[I]*, can be specified using a wildcard asterisk with the index
to effectively specify multiple values. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If N = the size of the vector, then an
asterisk with no numeric values means all indices from 1 to N. A
leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to N (inclusive). A middle
asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the
vector had been listed one by one. E.g. these 2 thermo_style commands
@ -372,6 +371,15 @@ creates a global vector with 6 values.
c_myTemp[1] c_myTemp[2] c_myTemp[3] &
c_myTemp[4] c_myTemp[5] c_myTemp[6]
.. note::
For a vector-style variable, only the wildcard forms "\*n" or
"m\*n" are allowed. You must specify the upper bound, because
vector-style variable lengths are not determined until the variable
is evaluated. If n is specified larger than the vector length
turns out to be, zeroes are output for missing vector values.
----------
The *c_ID* and *c_ID[I]* and *c_ID[I][J]* keywords allow global values

3
examples/ELASTIC_T/BORN_MATRIX/Silicon/output.in
View File

@ -136,5 +136,6 @@ variable C46 equal v_F46+v_B[20]
variable C56 equal v_F56+v_B[21]
thermo ${nthermo}
thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[1] v_B[2] v_B[3] v_B[4] v_B[5] v_B[6] v_B[7] v_B[8] v_B[12]
thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[*8] v_B[12]
thermo_modify norm no

6
src/ADIOS/Install.sh
View File

@ -31,17 +31,17 @@ done
if (test $1 = 1) then
CONFIGSCRIPT=none
if ( test `which adios2-config 2>> /dev/null` ) then
if ( type adios2-config > /dev/null 2>&1 ) then
CONFIGSCRIPT=adios2-config
elif ( ! test -z "$ADIOS2_DIR" ) then
if ( test `which $ADIOS2_DIR/bin/adios2-config` ) then
if ( type $ADIOS2_DIR/bin/adios2-config > /dev/null 2>&1 ) then
CONFIGSCRIPT=$ADIOS2_DIR/bin/adios2-config
else
echo "ERROR: ADIOS2_DIR environment variable is set but" \
"\$ADIOS2_DIR/bin/adios2-config does not exist"
fi
elif ( ! test -z "$ADIOS_DIR" ) then
if ( test `which $ADIOS_DIR/bin/adios2-config` ) then
if ( type $ADIOS_DIR/bin/adios2-config > /dev/null 2>&1 ) then
CONFIGSCRIPT=$ADIOS_DIR/bin/adios2-config
else
echo "ERROR: ADIOS_DIR environment variable is set but" \

4
src/ML-IAP/Install.sh
View File

@ -46,7 +46,7 @@ action mliap_model_python_couple.pyx python_impl.cpp
# edit 2 Makefile.package files to include/exclude package info
if (test $1 = 1) then
if (test "$(type cythonize 2> /dev/null)" != "" && test -e ../python_impl.cpp) then
if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then
if (test -e ../Makefile.package) then
sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package
fi
@ -69,7 +69,7 @@ elif (test $1 = 0) then
sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings
elif (test $1 = 2) then
if (type cythonize 2>&1 > /dev/null && test -e ../python_impl.cpp) then
if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then
if (test -e ../Makefile.package) then
sed -i -e 's/[^ \t]*-DMLIAP_PYTHON[^ \t]* //g' ../Makefile.package
fi

8
src/input.cpp
View File

@ -1195,11 +1195,9 @@ void Input::shell()
if (me == 0) {
for (int i = 1; i < narg; i++) {
rv = (platform::mkdir(arg[i]) < 0) ? errno : 0;
MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world);
errno = err;
if (err != 0)
error->warning(FLERR, "Shell command 'mkdir {}' failed with error '{}'",
arg[i],utils::getsyserror());
if (rv != 0)
error->warning(FLERR, "Shell command 'mkdir {}' failed with error '{}'", arg[i],
utils::getsyserror());
}
}
} else if (strcmp(arg[0],"mv") == 0) {

28
src/utils.cpp
View File

@ -19,11 +19,13 @@
#include "error.h"
#include "fix.h"
#include "fmt/chrono.h"
#include "input.h"
#include "memory.h"
#include "modify.h"
#include "text_file_reader.h"
#include "universe.h"
#include "update.h"
#include "variable.h"
#include <cctype>
#include <cerrno>
@ -631,7 +633,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod
// match compute, fix, or custom property array reference with a '*' wildcard
// number range in the first pair of square brackets
if (strmatch(word, "^[cf]_\\w+\\[\\d*\\*\\d*\\]") ||
if (strmatch(word, "^[cfv]_\\w+\\[\\d*\\*\\d*\\]") ||
strmatch(word, "^[id]2_\\w+\\[\\d*\\*\\d*\\]")) {
// split off the compute/fix/property ID, the wildcard and trailing text
@ -669,7 +671,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod
}
}
// fix
// fix
} else if (word[0] == 'f') {
auto fix = lmp->modify->get_fix_by_id(id);
@ -692,8 +694,25 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod
}
}
// only match custom array reference with a '*' wildcard
// number range in the first pair of square brackets
// vector variable
} else if (word[0] == 'v') {
int index = lmp->input->variable->find(id.c_str());
// check for global vector/array, peratom array, local array
if (index >= 0) {
if (mode == 0 && lmp->input->variable->vectorstyle(index)) {
utils::bounds(file, line, wc, 1, MAXSMALLINT, nlo, nhi, lmp->error);
if (nhi < MAXSMALLINT) {
nmax = nhi;
expandflag = 1;
}
}
}
// only match custom array reference with a '*' wildcard
// number range in the first pair of square brackets
} else if ((word[0] == 'i') || (word[0] == 'd')) {
int flag, cols;
@ -716,6 +735,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod
if (expandflag) {
// expand wild card string to nlo/nhi numbers
utils::bounds(file, line, wc, 1, nmax, nlo, nhi, lmp->error);
if (newarg + nhi - nlo + 1 > maxarg) {

3
src/utils.h
View File

@ -56,8 +56,7 @@ namespace utils {
* \param cmd name of the failing command
* \param error pointer to Error class instance (for abort) or nullptr */
[[noreturn]] void missing_cmd_args(const std::string &file, int line, const std::string &cmd,
Error *error);
void missing_cmd_args(const std::string &file, int line, const std::string &cmd, Error *error);
/* Internal function handling the argument list for logmesg(). */

125
tools/singularity/fedora36_mingw.def Normal file
View File

@ -0,0 +1,125 @@
BootStrap: docker
From: fedora:36
%post
dnf -y update
dnf -y install vim-enhanced git file make cmake patch which file Lmod \
ninja-build clang clang-tools-extra libomp-devel libubsan libasan libtsan \
diffutils dos2unix findutils rsync python-devel libjpeg-devel libpng-devel \
ccache gcc-c++ gcc-gfortran gdb valgrind eigen3-devel openblas-devel \
openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
readline-devel python3-pyyaml python3-Cython \
mingw-filesystem-base mingw32-nsis mingw-binutils-generic \
mingw32-filesystem mingw32-pkg-config \
mingw64-filesystem mingw64-pkg-config \
mingw32-crt mingw32-headers mingw32-binutils \
mingw64-crt mingw64-headers mingw64-binutils \
mingw32-cpp mingw32-gcc mingw32-gcc-gfortran mingw32-gcc-c++ \
mingw64-cpp mingw64-gcc mingw64-gcc-gfortran mingw64-gcc-c++ \
mingw32-libgomp mingw64-libgomp \
mingw32-winpthreads mingw64-winpthreads \
mingw32-eigen3 mingw64-eigen3 \
mingw32-fftw mingw64-fftw \
mingw32-libjpeg-turbo mingw64-libjpeg-turbo \
mingw32-libpng mingw64-libpng \
mingw32-python3 mingw64-python3 \
mingw32-python3-numpy mingw64-python3-numpy \
mingw32-python3-pyyaml mingw64-python3-pyyaml \
mingw32-python3-setuptools mingw64-python3-setuptools \
mingw32-readline mingw64-readline \
mingw32-termcap mingw64-termcap \
mingw32-zlib mingw64-zlib \
mingw32-zstd mingw64-zstd \
enchant python3-virtualenv doxygen latexmk \
texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \
texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng texlive-xindy \
blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel \
zstd libzstd-devel yaml-cpp-devel
dnf clean all
# enable Lmod and load MPI
source /usr/share/lmod/lmod/init/profile
module purge
module load mpi
# manually install Plumed
mkdir plumed
cd plumed
version=2.7.4
curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
tar -xzf plumed.tar.gz
cd plumed-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# create missing termcap pkgconfig files
cat > /usr/i686-w64-mingw32/sys-root/mingw/lib/pkgconfig/termcap.pc <<EOF
prefix=/usr/i686-w64-mingw32/sys-root/mingw
exec_prefix=/usr/i686-w64-mingw32/sys-root/mingw
libdir=/usr/i686-w64-mingw32/sys-root/mingw/lib
includedir=/usr/i686-w64-mingw32/sys-root/mingw/include
Name: Termcap
Description: GNU/MinGW terminal feature database
URL: ftp://ftp.gnu.org/gnu/termcap/
Version: 1.3
Libs: -L\${libdir} -ltermcap
Cflags:
EOF
cat > /usr/x86_64-w64-mingw32/sys-root/mingw/lib/pkgconfig/termcap.pc <<EOF
prefix=/usr/x86_64-w64-mingw32/sys-root/mingw
exec_prefix=/usr/x86_64-w64-mingw32/sys-root/mingw
libdir=/usr/x86_64-w64-mingw32/sys-root/mingw/lib
includedir=/usr/x86_64-w64-mingw32/sys-root/mingw/include
Name: Termcap
Description: GNU/MinGW terminal feature database
URL: ftp://ftp.gnu.org/gnu/termcap/
Version: 1.3
Libs: -L\${libdir} -ltermcap
Cflags:
EOF
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF
#!/bin/bash
PS1="[fedora36:\u@\h] \W> "
EOF
chmod 755 $CUSTOM_PROMPT_ENV
%environment
# we need to reset any module variables
# inherited from the host.
unset __LMOD_REF_COUNT__LMFILES_
unset __LMOD_REF_COUNT_PATH
unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
unset __LMOD_REF_COUNT_MANPATH
unset __LMOD_REF_COUNT_MODULEPATH
unset __LMOD_REF_COUNT_LOADEDMODULES
unset _LMFILES_
unset MODULEPATH
unset MODULESHOME
unset MODULEPATH_ROOT
unset LOADEDMODULES
unset LMOD_SYSTEM_DEFAULT_MODULES
# load MPI by default
. /etc/profile
module load mpi
# tell OpenMPI to not try using Infiniband
OMPI_MCA_btl="^openib"
# do not warn about unused components as this messes up testing
OMPI_MCA_btl_base_warn_component_unused="0"
export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused
%labels
Author akohlmey, rbberger

149
tools/singularity/ubuntu22.04.def Normal file
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@ -0,0 +1,149 @@
BootStrap: docker
From: ubuntu:22.04
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
# add-apt-repository ppa:openkim/latest
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \
bc \
build-essential \
ccache \
clang \
cmake \
cmake-curses-gui \
curl \
doxygen \
enchant-2 \
g++ \
gcc \
gfortran \
git \
hdf5-tools \
less \
libblas-dev \
libeigen3-dev \
libenchant-2-dev \
libfftw3-dev \
libgsl-dev \
libhdf5-serial-dev \
libhwloc-dev \
libjpeg-dev \
liblapack-dev \
libnetcdf-dev \
libomp-dev \
libopenblas-dev \
libnuma-dev \
libpng-dev \
libproj-dev \
libreadline-dev \
libvtk9-dev \
libyaml-dev \
libzstd-dev \
make \
mpi-default-bin \
mpi-default-dev \
ninja-build \
python3-dev \
python3-pip \
python3-pkg-resources \
python3-setuptools \
python3-virtualenv \
python3-venv \
rsync \
ssh \
texlive \
texlive-latex-recommended \
texlive-formats-extra \
texlive-pictures \
texlive-publishers \
texlive-science \
dvipng \
latexmk \
xindy \
vim-nox \
virtualenv \
voro++-dev \
wget \
xxd \
valgrind \
gdb \
zstd \
libyaml-cpp-dev \
libkim-api-dev \
gpg-agent \
# openkim-models
# ###########################################################################
# # KIM-API
# ###########################################################################
#
# # workaround for installing files in /usr/share/doc inside of a container
# sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
# apt-get install -y libkim-api-doc
# sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
#
# # install KIM models
# KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples
# gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz
# gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz
#
# kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003
# kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ
# kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar
# kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ
# kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003
# kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu
###########################################################################
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.7.4
mkdir plumed
cd plumed
curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_PKG_VERSION}/plumed-src-${PLUMED_PKG_VERSION}.tgz
tar -xzf plumed.tar.gz
cd plumed-${PLUMED_PKG_VERSION}
./configure --disable-doc --prefix=/usr
make
make install
cd ../../
rm -rvf plumed
###########################################################################
# Customizations
###########################################################################
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF
#!/bin/bash
PS1="[ubuntu22.04:\u@\h] \W> "
EOF
chmod 755 $CUSTOM_PROMPT_ENV
###########################################################################
# Cleanup
###########################################################################
# clean cache
rm -rf /var/lib/apt/lists/*
%environment
LC_ALL=C
export LC_ALL
export PATH=/usr/lib/ccache:$PATH
# tell OpenMPI to not try using Infiniband
OMPI_MCA_btl="^openib"
# do not warn about unused components as this messes up testing
OMPI_MCA_btl_base_warn_component_unused="0"
export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused
%labels
Author akohlmey, rbberger

4
unittest/cplusplus/CMakeLists.txt
View File

@ -8,6 +8,10 @@ add_executable(test_input_class test_input_class.cpp)
target_link_libraries(test_input_class PRIVATE lammps GTest::GTestMain)
add_test(NAME InputClass COMMAND test_input_class)
add_executable(test_advanced_utils test_advanced_utils.cpp)
target_link_libraries(test_advanced_utils PRIVATE lammps GTest::GMock)
add_test(NAME AdvancedUtils COMMAND test_advanced_utils)
add_executable(test_error_class test_error_class.cpp)
target_link_libraries(test_error_class PRIVATE lammps GTest::GMock)
add_test(NAME ErrorClass COMMAND test_error_class)

247
unittest/cplusplus/test_advanced_utils.cpp Normal file
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@ -0,0 +1,247 @@
// unit tests for utils:: functions requiring a LAMMPS
#include "error.h"
#include "input.h"
#include "lammps.h"
#include "memory.h"
#include "utils.h"
#include "../testing/core.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <string>
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
namespace LAMMPS_NS {
class Advanced_utils : public LAMMPSTest {
protected:
Error *error;
void SetUp() override
{
testbinary = "AdvancedUtils";
LAMMPSTest::SetUp();
error = lmp->error;
}
void atomic_system()
{
BEGIN_HIDE_OUTPUT();
command("units real");
command("lattice sc 1.0 origin 0.125 0.125 0.125");
command("region box block -2 2 -2 2 -2 2");
command("create_box 8 box");
command("create_atoms 1 box");
command("pair_style zero 3.5");
command("pair_coeff * *");
command("mass * 1.0");
command("region left block -2.0 -1.0 INF INF INF INF");
command("region right block 0.5 2.0 INF INF INF INF");
command("region top block INF INF -2.0 -1.0 INF INF");
command("set region left type 2");
command("set region right type 3");
END_HIDE_OUTPUT();
}
};
TEST_F(Advanced_utils, missing_cmd_args)
{
auto output = CAPTURE_OUTPUT([&] {
utils::missing_cmd_args(FLERR, "dummy", nullptr);
});
EXPECT_EQ(output, "");
TEST_FAILURE("ERROR: Illegal dummy command: missing argument",
utils::missing_cmd_args(FLERR, "dummy", error););
};
TEST_F(Advanced_utils, logmesg)
{
auto output = CAPTURE_OUTPUT([&] {
utils::logmesg(lmp, "test message");
});
EXPECT_EQ(output, "test message");
output = CAPTURE_OUTPUT([&] {
utils::logmesg(lmp, "test message from test {}", testbinary);
});
EXPECT_EQ(output, "test message from test " + testbinary);
};
// death tests only. the other cases are tested in the basic utils unit tester
TEST_F(Advanced_utils, bounds_int_fail)
{
int nlo, nhi;
TEST_FAILURE("ERROR: Invalid range string: 1x ",
utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: -1 ",
utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: \\+1 ",
utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: 1:3 ",
utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: \\? ",
utils::bounds(FLERR, "?", -10, 5, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: 3\\*:2 ",
utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, error););
}
TEST_F(Advanced_utils, bounds_bigint_fail)
{
bigint nlo, nhi;
TEST_FAILURE("ERROR: Invalid range string: 1x ",
utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: -1 ",
utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: \\+1 ",
utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: 1:3 ",
utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: \\? ",
utils::bounds(FLERR, "?", -10, 5, nlo, nhi, error););
TEST_FAILURE("ERROR: Invalid range string: 3\\*:2 ",
utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, error););
}
TEST_F(Advanced_utils, expand_args)
{
atomic_system();
BEGIN_CAPTURE_OUTPUT();
command("compute temp all temp");
command("variable temp vector c_temp");
command("variable step equal step");
command("variable pe equal pe");
command("variable pe equal pe");
command("variable epair equal epair");
command("compute gofr all rdf 20 1 1 1 2");
command("fix 1 all ave/time 1 1 1 v_step v_pe v_epair");
command("fix 2 all nve");
command("run 1 post no");
auto output = END_CAPTURE_OUTPUT();
char **args, **earg;
constexpr int oarg = 9;
args = new char *[oarg];
args[0] = utils::strdup("v_step");
args[1] = utils::strdup("c_temp");
args[2] = utils::strdup("f_1[*]");
args[3] = utils::strdup("c_temp[2*4]");
args[4] = utils::strdup("v_temp[*4]");
args[5] = utils::strdup("c_gofr[3*]");
args[6] = utils::strdup("c_gofr[1][*]");
args[7] = utils::strdup("c_gofr[*2][2]");
args[8] = utils::strdup("c_gofr[*][*]");
auto narg = utils::expand_args(FLERR, oarg, args, 0, earg, lmp);
EXPECT_EQ(narg, 16);
EXPECT_STREQ(earg[0], "v_step");
EXPECT_STREQ(earg[1], "c_temp");
EXPECT_STREQ(earg[2], "f_1[1]");
EXPECT_STREQ(earg[3], "f_1[2]");
EXPECT_STREQ(earg[4], "f_1[3]");
EXPECT_STREQ(earg[5], "c_temp[2]");
EXPECT_STREQ(earg[6], "c_temp[3]");
EXPECT_STREQ(earg[7], "c_temp[4]");
EXPECT_STREQ(earg[8], "v_temp[1]");
EXPECT_STREQ(earg[9], "v_temp[2]");
EXPECT_STREQ(earg[10], "v_temp[3]");
EXPECT_STREQ(earg[11], "v_temp[4]");
EXPECT_STREQ(earg[12], "c_gofr[3*]");
EXPECT_STREQ(earg[13], "c_gofr[1][*]");
EXPECT_STREQ(earg[14], "c_gofr[*2][2]");
EXPECT_STREQ(earg[15], "c_gofr[*][*]");
for (int i = 0; i < narg; ++i)
delete[] earg[i];
lmp->memory->sfree(earg);
narg = utils::expand_args(FLERR, oarg, args, 1, earg, lmp);
EXPECT_EQ(narg, 16);
EXPECT_NE(args, earg);
EXPECT_STREQ(earg[0], "v_step");
EXPECT_STREQ(earg[1], "c_temp");
EXPECT_STREQ(earg[2], "f_1[*]");
EXPECT_STREQ(earg[3], "c_temp[2*4]");
EXPECT_STREQ(earg[4], "v_temp[*4]");
EXPECT_STREQ(earg[5], "c_gofr[3]");
EXPECT_STREQ(earg[6], "c_gofr[4]");
EXPECT_STREQ(earg[7], "c_gofr[5]");
EXPECT_STREQ(earg[8], "c_gofr[1][*]");
EXPECT_STREQ(earg[9], "c_gofr[1][2]");
EXPECT_STREQ(earg[10], "c_gofr[2][2]");
EXPECT_STREQ(earg[11], "c_gofr[1][*]");
EXPECT_STREQ(earg[12], "c_gofr[2][*]");
EXPECT_STREQ(earg[13], "c_gofr[3][*]");
EXPECT_STREQ(earg[14], "c_gofr[4][*]");
EXPECT_STREQ(earg[15], "c_gofr[5][*]");
for (int i = 0; i < narg; ++i)
delete[] earg[i];
lmp->memory->sfree(earg);
args[3][9] = '9';
TEST_FAILURE("ERROR: Numeric index 9 is out of bounds \\(1-6\\).*",
utils::expand_args(FLERR, oarg, args, 0, earg, lmp););
args[3][9] = '4';
args[5][7] = '9';
TEST_FAILURE("ERROR: Numeric index 9 is out of bounds \\(1-5\\).*",
utils::expand_args(FLERR, oarg, args, 1, earg, lmp););
args[5][7] = '3';
delete[] args[4];
args[4] = utils::strdup("v_temp[2*]");
narg = utils::expand_args(FLERR, oarg, args, 0, earg, lmp);
EXPECT_EQ(narg, 13);
EXPECT_STREQ(earg[0], "v_step");
EXPECT_STREQ(earg[1], "c_temp");
EXPECT_STREQ(earg[2], "f_1[1]");
EXPECT_STREQ(earg[3], "f_1[2]");
EXPECT_STREQ(earg[4], "f_1[3]");
EXPECT_STREQ(earg[5], "c_temp[2]");
EXPECT_STREQ(earg[6], "c_temp[3]");
EXPECT_STREQ(earg[7], "c_temp[4]");
EXPECT_STREQ(earg[8], "v_temp[2*]");
EXPECT_STREQ(earg[9], "c_gofr[3*]");
EXPECT_STREQ(earg[10], "c_gofr[1][*]");
EXPECT_STREQ(earg[11], "c_gofr[*2][2]");
EXPECT_STREQ(earg[12], "c_gofr[*][*]");
for (int i = 0; i < narg; ++i)
delete[] earg[i];
lmp->memory->sfree(earg);
for (int i = 0; i < oarg; ++i)
delete[] args[i];
delete[] args;
}
} // namespace LAMMPS_NS
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
if (platform::mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions())
std::cout << "Warning: using OpenMPI without exceptions. Death tests will be skipped\n";
// handle arguments passed via environment variable
if (const char *var = getenv("TEST_ARGS")) {
std::vector<std::string> env = utils::split_words(var);
for (auto arg : env) {
if (arg == "-v") {
verbose = true;
}
}
}
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
int rv = RUN_ALL_TESTS();
MPI_Finalize();
return rv;
}

5
unittest/cplusplus/test_error_class.cpp
View File

@ -1,4 +1,4 @@
// unit tests for issuing command to a LAMMPS instance through the Input class
// unit tests for public member functions of the Error class
#include "error.h"
#include "info.h"
@ -129,8 +129,7 @@ int main(int argc, char **argv)
::testing::InitGoogleMock(&argc, argv);
if (platform::mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions())
std::cout << "Warning: using OpenMPI without exceptions. "
"Death tests will be skipped\n";
std::cout << "Warning: using OpenMPI without exceptions. Death tests will be skipped\n";
// handle arguments passed via environment variable
if (const char *var = getenv("TEST_ARGS")) {

6
unittest/utils/test_utils.cpp
View File

@ -746,6 +746,12 @@ TEST(Utils, boundsbig_case3)
ASSERT_EQ(nhi, -1);
}
TEST(Utils, errorurl)
{
auto errmesg = utils::errorurl(10);
ASSERT_THAT(errmesg, Eq("\nFor more information see https://docs.lammps.org/err0010"));
}
TEST(Utils, getsyserror)
{
#if defined(__linux__)