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Merge branch 'fortran-further-tinkering' of github.com:hammondkd/lammps into fortran-further-tinkering

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This commit is contained in:
Karl Hammond
2022-10-05 14:30:30 -05:00
parent e3b5514b62 723255bf7e
commit 3a4d4b0756
18 changed files with 580 additions and 187 deletions
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5
cmake/CMakeLists.txt
View File

@ -12,6 +12,11 @@ endif()
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
########################################
project(lammps CXX)

25
cmake/Modules/Packages/MDI.cmake
View File

@ -49,6 +49,14 @@ if(DOWNLOAD_MDI)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
endif()
# python plugins are not supported and thus must be always off on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
unset(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_CROSSCOMPILING)
set(CMAKE_INSTALL_LIBDIR lib)
endif()
endif()
# download/ build MDI library
# always build static library with -fpic
@ -57,8 +65,9 @@ if(DOWNLOAD_MDI)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL_MD5 ${MDI_MD5}
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
CMAKE_ARGS
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
@ -70,22 +79,22 @@ if(DOWNLOAD_MDI)
-Dplugins=ON
-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
UPDATE_COMMAND ""
INSTALL_COMMAND ""
BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
INSTALL_COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/src/mdi_build-build --target install
BUILD_BYPRODUCTS "${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
)
# where is the compiled library?
ExternalProject_get_property(mdi_build BINARY_DIR)
set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
ExternalProject_get_property(mdi_build PREFIX)
# workaround for older CMake versions
file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
file(MAKE_DIRECTORY ${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi)
file(MAKE_DIRECTORY ${PREFIX}/include/mdi)
# create imported target for the MDI library
add_library(LAMMPS::MDI UNKNOWN IMPORTED)
add_dependencies(LAMMPS::MDI mdi_build)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
IMPORTED_LOCATION "${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include/mdi
)
set(MDI_DEP_LIBS "")

34
doc/src/Python_neighbor.rst
View File

@ -38,6 +38,40 @@ using the NumPy access method.
for n in np.nditer(nlist):
print(" atom {} with ID {}".format(n,tags[n]))
Another example for extracting a full neighbor list without evaluating a
potential is shown below.
.. code-block:: python
from lammps import lammps
import numpy as np
lmp = lammps()
lmp.commands_string("""
newton off
region box block -2 2 -2 2 -2 2
lattice fcc 1.0
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style zero 1.0 full
pair_coeff * *
run 0 post no""")
# look up the neighbor list
nlidx = lmp.find_pair_neighlist('zero')
nl = lmp.numpy.get_neighlist(nlidx)
tags = lmp.extract_atom('id')
print("full neighbor list with {} entries".format(nl.size))
# print neighbor list contents
for i in range(0,nl.size):
idx, nlist = nl.get(i)
print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
if nlist.size > 0:
for n in np.nditer(nlist):
pass
print(" atom {} with ID {}".format(n,tags[n]))
**Methods:**
* :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index

67
doc/src/pair_list.rst
View File

@ -30,15 +30,17 @@ Description
"""""""""""
Style *list* computes interactions between explicitly listed pairs of
atoms with the option to select functional form and parameters for
each individual pair. Because the parameters are set in the list
file, the pair_coeff command has no parameters (but still needs to be
provided). The *check* and *nocheck* keywords enable/disable a test
that checks whether all listed bonds were present and computed.
atoms with the option to select functional form and parameters for each
individual pair. Because the parameters are set in the list file, the
pair_coeff command has no parameters (but still needs to be provided).
The *check* and *nocheck* keywords enable/disable tests that checks
whether all listed pairs of atom IDs were present and the interactions
computed. If *nocheck* is set and either atom ID is not present, the
interaction is skipped.
This pair style can be thought of as a hybrid between bonded,
non-bonded, and restraint interactions. It will typically be used as
an additional interaction within the *hybrid/overlay* pair style. It
non-bonded, and restraint interactions. It will typically be used as an
additional interaction within the *hybrid/overlay* pair style. It
currently supports three interaction styles: a 12-6 Lennard-Jones, a
Morse and a harmonic potential.
@ -55,10 +57,10 @@ The format of the list file is as follows:
ID2 = atom ID of second atom
style = style of interaction
coeffs = list of coeffs
cutoff = cutoff for interaction (optional)
cutoff = cutoff for interaction (optional, except for style *quartic*)
The cutoff parameter is optional. If not specified, the global cutoff
is used.
The cutoff parameter is optional for all but the *quartic* interactions.
If it is not specified, the global cutoff is used.
Here is an example file:
@ -69,6 +71,7 @@ Here is an example file:
15 259 lj126 1.0 1.0 50.0
15 603 morse 10.0 1.2 2.0 10.0 # and another comment
18 470 harmonic 50.0 1.2 5.0
19 332 quartic 5.0 -1.2 1.2 5.0
The style *lj126* computes pairwise interactions with the formula
@ -85,7 +88,7 @@ The style *morse* computes pairwise interactions with the formula
.. math::
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c
E = D_0 \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 \qquad r < r_c
and the coefficients:
@ -106,6 +109,21 @@ and the coefficients:
Note that the usual 1/2 factor is included in :math:`K`.
The style *quartic* computes pairwise interactions with the formula
.. math::
E = K (r - r_c)^2 (r - r_c -b_1) (r - r_c - b_2) \qquad r < r_c
and the coefficients:
* :math:`K` (energy units)
* :math:`b_1` (distance units)
* :math:`b_2` (distance units)
* :math:`r_c` (distance units)
Note that the per list entry cutoff :math:`r_c` is **required** for *quartic* interactions.
----------
Mixing, shift, table, tail correction, restart, rRESPA info
@ -120,8 +138,9 @@ pair style.
The :doc:`pair_modify <pair_modify>` table and tail options are not
relevant for this pair style.
This pair style does not write its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need
to be specified in an input script that reads a restart file.
This pair style does not write its information to :doc:`binary restart
files <restart>`, so pair_style and pair_coeff commands need to be
specified in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
@ -134,16 +153,17 @@ Restrictions
This pair style does not use a neighbor list and instead identifies
atoms by their IDs. This has two consequences: 1) The cutoff has to be
chosen sufficiently large, so that the second atom of a pair has to be
a ghost atom on the same node on which the first atom is local;
otherwise the interaction will be skipped. You can use the *check*
option to detect, if interactions are missing. 2) Unlike other pair
styles in LAMMPS, an atom I will not interact with multiple images of
atom J (assuming the images are within the cutoff distance), but only
with the nearest image.
chosen sufficiently large, so that the second atom of a pair has to be a
ghost atom on the same node on which the first atom is local; otherwise
the interaction will be skipped. You can use the *check* option to
detect, if interactions are missing. 2) Unlike other pair styles in
LAMMPS, an atom I will not interact with multiple images of atom J
(assuming the images are within the cutoff distance), but only with the
closest image.
This style is part of the MISC package. It is only enabled if
LAMMPS is build with that package. See the :doc:`Build package <Build_package>` page on for more info.
This style is part of the MISC package. It is only enabled if LAMMPS is
build with that package. See the :doc:`Build package <Build_package>`
page on for more info.
Related commands
""""""""""""""""
@ -151,8 +171,9 @@ Related commands
:doc:`pair_coeff <pair_coeff>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`pair_style lj/cut <pair_lj>`,
:doc:`pair_style morse <pair_morse>`,
:doc:`bond_style morse <bond_morse>`,
:doc:`bond_style harmonic <bond_harmonic>`
:doc:`bond_style quartic <bond_quartic>`
Default
"""""""

6
doc/src/pair_zero.rst
View File

@ -8,11 +8,12 @@ Syntax
.. code-block:: LAMMPS
pair_style zero cutoff [nocoeff]
pair_style zero cutoff [nocoeff] [full]
* zero = style name of this pair style
* cutoff = global cutoff (distance units)
* nocoeff = ignore all pair_coeff parameters (optional)
* full = build full neighbor list (optional)
Examples
""""""""
@ -45,6 +46,9 @@ section for any pair style. Similarly, any pair_coeff commands
will only be checked for the atom type numbers and the rest ignored.
In this case, only the global cutoff will be used.
The optional *full* flag builds a full neighbor list instead of the default
half neighbor list.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
above, or in the data file or restart files read by the

12
fortran/lammps.f90
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@ -1134,7 +1134,7 @@ CONTAINS
TYPE(lammps_variable_data) :: variable_data
TYPE(c_ptr) :: Cptr, Cname, Cgroup, Cveclength
INTEGER :: length, i
INTEGER(c_size_t) :: length, i
CHARACTER(KIND=c_char, LEN=1), DIMENSION(:), POINTER :: Cstring
INTEGER(c_int) :: datatype
REAL(c_double), POINTER :: double => NULL()
@ -1370,7 +1370,6 @@ CONTAINS
INTEGER(c_int) :: ndata
TYPE(c_ptr) :: Cdata, Cname, Cids
INTEGER(c_int), PARAMETER :: Ctype = 0_c_int
CHARACTER(LEN=100) :: error_msg
IF (count /= 1 .AND. count /= 3) THEN
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
@ -1401,7 +1400,6 @@ CONTAINS
INTEGER(c_int) :: ndata
TYPE(c_ptr) :: Cdata, Cname, Cids
INTEGER(c_int), PARAMETER :: Ctype = 1_c_int
CHARACTER(LEN=100) :: error_msg
IF (count /= 1 .AND. count /= 3) THEN
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
@ -1494,7 +1492,6 @@ CONTAINS
INTEGER(c_int), PARAMETER :: Ctype = 0_c_int
INTEGER(c_int) :: Cndata, Ccount
TYPE(c_ptr) :: Cdata, Cname, Cids
CHARACTER(LEN=100) :: error_msg
Cndata = SIZE(ids, KIND=c_int)
Ccount = SIZE(data, KIND=c_int) / Cndata
@ -1519,7 +1516,6 @@ CONTAINS
INTEGER(c_int), PARAMETER :: Ctype = 1_c_int
INTEGER(c_int) :: Cndata, Ccount
TYPE(c_ptr) :: Cdata, Cname, Cids
CHARACTER(LEN=100) :: error_msg
Cndata = SIZE(ids, KIND=c_int)
Ccount = SIZE(data, KIND=c_int) / Cndata
@ -1628,7 +1624,7 @@ CONTAINS
INTEGER(c_int) :: Cidx, Csuccess
TYPE(c_ptr) :: Cptr
CHARACTER(LEN=1,KIND=c_char), TARGET :: Cbuffer(LEN(buffer)+1)
INTEGER :: i, strlen
INTEGER(c_size_t) :: i, strlen
Cidx = idx - 1
Cptr = C_LOC(Cbuffer(1))
@ -1698,8 +1694,8 @@ CONTAINS
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*), INTENT(OUT) :: buffer
INTEGER, INTENT(OUT), OPTIONAL :: status
INTEGER(c_int) :: buflen, Cstatus, i
INTEGER(c_size_t) :: length
INTEGER(c_int) :: buflen, Cstatus
INTEGER(c_size_t) :: i, length
TYPE(c_ptr) :: Cptr
CHARACTER(LEN=1, KIND=c_char), POINTER :: c_string(:)

144
src/MISC/pair_list.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -22,27 +21,33 @@
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_special.h"
#include "memory.h"
#include "text_file_reader.h"
#include <cstring>
#include <cmath>
#include <cstring>
#include <exception>
#include <map>
using namespace LAMMPS_NS;
using MathSpecial::square;
enum { NONE = 0, HARM, MORSE, LJ126 };
enum { NONE = 0, HARM, MORSE, LJ126, QUARTIC };
// clang-format off
static std::map<std::string, int> stylename = {
{"none", NONE},
{"harmonic", HARM},
{"morse", MORSE},
{ "lj126", LJ126 }
{"lj126", LJ126},
{"quartic", QUARTIC}
};
// clang-format on
// fast power function for integer exponent > 0
static double mypow(double x, int n) {
static double mypow(double x, int n)
{
double yy;
if (x == 0.0) return 0.0;
@ -53,7 +58,9 @@ static double mypow(double x, int n) {
return yy;
}
typedef struct { double x,y,z; } dbl3_t;
typedef struct {
double x, y, z;
} dbl3_t;
/* ---------------------------------------------------------------------- */
@ -86,7 +93,15 @@ void PairList::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
// get maximum allowed tag.
bigint maxtag_one, maxtag;
maxtag_one = maxtag = 0;
const int nlocal = atom->nlocal;
const tagint *_noalias const tag = atom->tag;
for (int i = 0; i < nlocal; ++i) maxtag_one = MAX(maxtag_one, tag[i]);
MPI_Allreduce(&maxtag_one, &maxtag, 1, MPI_LMP_TAGINT, MPI_MAX, world);
const int newton_pair = force->newton_pair;
const dbl3_t *_noalias const x = (dbl3_t *) atom->x[0];
dbl3_t *_noalias const f = (dbl3_t *) atom->f[0]; // NOLINT
@ -97,6 +112,21 @@ void PairList::compute(int eflag, int vflag)
int pc = 0;
for (int n = 0; n < npairs; ++n) {
const list_param &par = params[n];
// can only use valid tags or else atom->map() below will segfault.
if ((par.id1 < 1) || (par.id1 > maxtag)) {
if (check_flag)
error->all(FLERR, "Invalid pair list atom ID {}", par.id1);
else
continue;
}
if ((par.id2 < 1) || (par.id2 > maxtag)) {
if (check_flag)
error->all(FLERR, "Invalid pair list atom ID {}", par.id2);
else
continue;
}
i = atom->map(par.id1);
j = atom->map(par.id2);
@ -133,30 +163,36 @@ void PairList::compute(int eflag, int vflag)
const double dr = par.param.harm.r0 - r;
fpair = 2.0 * par.param.harm.k * dr / r;
if (eflag_either)
epair = par.param.harm.k*dr*dr - par.offset;
if (eflag_either) epair = par.param.harm.k * dr * dr - par.offset;
} else if (par.style == MORSE) {
const double r = sqrt(rsq);
const double dr = par.param.morse.r0 - r;
const double dexp = exp(par.param.morse.alpha * dr);
fpair = 2.0*par.param.morse.d0*par.param.morse.alpha
* (dexp*dexp - dexp) / r;
const double dr = r - par.param.morse.r0;
const double dexp = exp(-par.param.morse.alpha * dr);
fpair = 2.0 * par.param.morse.d0 * par.param.morse.alpha * (dexp * dexp - dexp) / r;
if (eflag_either)
epair = par.param.morse.d0 * (dexp*dexp - 2.0*dexp) - par.offset;
if (eflag_either) epair = par.param.morse.d0 * (dexp * dexp - 2.0 * dexp + 1.0) - par.offset;
} else if (par.style == LJ126) {
const double r6inv = r2inv * r2inv * r2inv;
const double sig6 = mypow(par.param.lj126.sigma, 6);
fpair = 24.0*par.param.lj126.epsilon*r6inv
* (2.0*sig6*sig6*r6inv - sig6) * r2inv;
fpair = 24.0 * par.param.lj126.epsilon * r6inv * (2.0 * sig6 * sig6 * r6inv - sig6) * r2inv;
if (eflag_either)
epair = 4.0*par.param.lj126.epsilon*r6inv
* (sig6*sig6*r6inv - sig6) - par.offset;
epair = 4.0 * par.param.lj126.epsilon * r6inv * (sig6 * sig6 * r6inv - sig6) - par.offset;
} else if (par.style == QUARTIC) {
const double r = sqrt(rsq);
double dr = r - sqrt(par.cutsq);
double ra = dr - par.param.quartic.b1;
double rb = dr - par.param.quartic.b2;
double r2 = dr * dr;
fpair = -par.param.quartic.k / r * (r2 * (ra + rb) + 2.0 * dr * ra * rb);
if (eflag_either) epair = par.param.quartic.k * r2 * ra * rb;
}
if (newton_pair || i < nlocal) {
@ -180,7 +216,7 @@ void PairList::compute(int eflag, int vflag)
int tmp;
MPI_Allreduce(&pc, &tmp, 1, MPI_INT, MPI_SUM, world);
if (tmp != 2 * npairs)
error->all(FLERR,"Not all pairs processed in pair_style list");
error->all(FLERR, "Not all pairs processed in pair_style list: {} vs {}", tmp, 2 * npairs);
}
}
@ -191,14 +227,13 @@ void PairList::compute(int eflag, int vflag)
void PairList::allocate()
{
allocated = 1;
int n = atom->ntypes;
int np1 = atom->ntypes + 1;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(setflag, np1, np1, "pair:setflag");
for (int i = 1; i < np1; i++)
for (int j = i; j < np1; j++) setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cutsq, np1, np1, "pair:cutsq");
}
/* ----------------------------------------------------------------------
@ -207,13 +242,19 @@ void PairList::allocate()
void PairList::settings(int narg, char **arg)
{
if (narg < 2)
error->all(FLERR,"Illegal pair_style command");
if (narg < 2) utils::missing_cmd_args(FLERR, "pair_style list", error);
cut_global = utils::numeric(FLERR, arg[1], false, lmp);
if (narg > 2) {
if (strcmp(arg[2],"nocheck") == 0) check_flag = 0;
if (strcmp(arg[2],"check") == 0) check_flag = 1;
int iarg = 2;
while (iarg < narg) {
if (strcmp(arg[iarg], "nocheck") == 0) {
check_flag = 0;
++iarg;
} else if (strcmp(arg[2], "check") == 0) {
check_flag = 1;
++iarg;
} else
error->all(FLERR, "Unknown pair style list keyword: {}", arg[iarg]);
}
std::vector<int> mystyles;
@ -221,13 +262,15 @@ void PairList::settings(int narg, char **arg)
// read and parse potential file only on MPI rank 0.
if (comm->me == 0) {
int nharm, nmorse, nlj126, nskipped;
int nharm, nmorse, nlj126, nquartic, nskipped;
FILE *fp = utils::open_potential(arg[0], lmp, nullptr);
if (!fp)
error->one(FLERR, "Error opening pair list coeffs file {}: {}", arg[0], utils::getsyserror());
TextFileReader reader(fp, "pair list coeffs");
npairs = nharm = nmorse = nlj126 = nskipped = 0;
npairs = nharm = nmorse = nlj126 = nquartic = nskipped = 0;
char *line;
try {
char *line;
while ((line = reader.next_line())) {
ValueTokenizer values(line);
list_param oneparam;
@ -258,6 +301,15 @@ void PairList::settings(int narg, char **arg)
++nlj126;
break;
case QUARTIC:
oneparam.param.quartic.k = values.next_double();
oneparam.param.quartic.b1 = values.next_double();
oneparam.param.quartic.b2 = values.next_double();
if (!values.has_next())
throw FileReaderException("Must specify individual cutoff for quartic interaction");
++nquartic;
break;
case NONE: // fallthrough
error->warning(FLERR, "Skipping unrecognized pair list potential entry: {}",
utils::trim(line));
@ -265,17 +317,19 @@ void PairList::settings(int narg, char **arg)
break;
}
if (values.has_next())
oneparam.cutsq = values.next_double();
oneparam.cutsq = square(values.next_double());
else
oneparam.cutsq = cut_global * cut_global;
myparams.push_back(oneparam);
}
} catch (std::exception &e) {
error->one(FLERR,"Error reading pair list coeffs file: {}", e.what());
error->one(FLERR, "Error reading pair list coeffs file: {}\n{}", e.what(), line);
}
utils::logmesg(lmp, "Read {} ({}/{}/{}) interacting pair lines from {}. "
"{} skipped entries.\n", npairs, nharm, nmorse, nlj126, arg[0], nskipped);
utils::logmesg(lmp,
"Read {} ({}/{}/{}/{}) interacting pair lines from {}. "
"{} skipped entries.\n",
npairs, nharm, nmorse, nlj126, nquartic, arg[0], nskipped);
memory->create(params, npairs, "pair_list:params");
memcpy(params, myparams.data(), npairs * sizeof(list_param));
@ -287,12 +341,12 @@ void PairList::settings(int narg, char **arg)
}
/* ----------------------------------------------------------------------
there are no coeffs to be set, but we need to update setflag and pretend
there are no coeffs to be set, but we need to update setflag and pretend there are
------------------------------------------------------------------------- */
void PairList::coeff(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Incorrect args for pair coefficients");
if (narg < 2) utils::missing_cmd_args(FLERR, "pair_coeff list", error);
if (!allocated) allocate();
int ilo, ihi, jlo, jhi;
@ -316,11 +370,9 @@ void PairList::coeff(int narg, char **arg)
void PairList::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style list requires atom IDs");
if (atom->tag_enable == 0) error->all(FLERR, "Pair style list requires atom IDs");
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR,"Pair style list requires an atom map");
if (atom->map_style == Atom::MAP_NONE) error->all(FLERR, "Pair style list requires an atom map");
if (offset_flag) {
for (int n = 0; n < npairs; ++n) {
@ -333,12 +385,16 @@ void PairList::init_style()
} else if (par.style == MORSE) {
const double dr = par.param.morse.r0 - sqrt(par.cutsq);
const double dexp = exp(par.param.morse.alpha * dr);
par.offset = par.param.morse.d0 * (dexp*dexp - 2.0*dexp);
par.offset = par.param.morse.d0 * (dexp * dexp - 2.0 * dexp - 1.0);
} else if (par.style == LJ126) {
const double r6inv = par.cutsq * par.cutsq * par.cutsq;
const double sig6 = mypow(par.param.lj126.sigma, 6);
par.offset = 4.0 * par.param.lj126.epsilon * r6inv * (sig6 * sig6 * r6inv - sig6);
} else if (par.style == QUARTIC) {
// the offset is always 0 at rc
par.offset = 0.0;
}
}
}

5
src/MISC/pair_list.h
View File

@ -49,11 +49,16 @@ class PairList : public Pair {
struct lj126_p {
double epsilon, sigma;
};
struct quartic_p {
double k, b1, b2;
};
union param_u {
harm_p harm;
morse_p morse;
lj126_p lj126;
quartic_p quartic;
};
struct list_param {

2
src/fix_ave_time.cpp
View File

@ -895,7 +895,7 @@ void FixAveTime::invoke_vector(bigint ntimestep)
int FixAveTime::column_length(int dynamic)
{
int m,length,lengthone;
int length,lengthone;
// determine nrows for static values

35
src/pair_zero.cpp
View File

@ -21,6 +21,8 @@
#include "comm.h"
#include "error.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cstring>
@ -34,6 +36,7 @@ PairZero::PairZero(LAMMPS *lmp) : Pair(lmp)
writedata = 1;
single_enable = 1;
respa_enable = 1;
fullneighflag = 0;
}
/* ---------------------------------------------------------------------- */
@ -85,14 +88,24 @@ void PairZero::allocate()
void PairZero::settings(int narg, char **arg)
{
if ((narg != 1) && (narg != 2)) error->all(FLERR, "Illegal pair_style command");
if (narg < 1) utils::missing_cmd_args(FLERR, "pair_style zero", error);
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
if (narg == 2) {
if (strcmp("nocoeff", arg[1]) == 0)
// reset to defaults
coeffflag = 1;
fullneighflag = 0;
int iarg = 1;
while (iarg < narg) {
if (strcmp("nocoeff", arg[iarg]) == 0) {
coeffflag = 0;
else
error->all(FLERR, "Illegal pair_style command");
++iarg;
} else if (strcmp("full", arg[iarg]) == 0) {
fullneighflag = 1;
++iarg;
} else
error->all(FLERR, "Unknown pair style zero option {}", arg[iarg]);
}
// reset cutoffs that have been explicitly set
@ -134,6 +147,18 @@ void PairZero::coeff(int narg, char **arg)
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairZero::init_style()
{
if (fullneighflag)
neighbor->add_request(this, NeighConst::REQ_FULL);
else
neighbor->add_request(this, NeighConst::REQ_DEFAULT);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */

4
src/pair_zero.h
View File

@ -42,6 +42,7 @@ class PairZero : public Pair {
void compute_outer(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
@ -55,11 +56,10 @@ class PairZero : public Pair {
double cut_global;
double **cut;
int coeffflag;
int fullneighflag; // 0 for half list, 1 for full list
virtual void allocate();
};
} // namespace LAMMPS_NS
#endif
#endif

4
unittest/force-styles/CMakeLists.txt
View File

@ -260,3 +260,7 @@ if(MLIAP_ENABLE_PYTHON AND (NOT WIN32))
set_tests_properties(TestMliapPyUnified PROPERTIES ENVIRONMENT "PYTHONPATH=${LAMMPS_PYTHON_DIR};PYTHONDONTWRITEBYTECODE=1")
endif()
add_executable(test_pair_list test_pair_list.cpp)
target_link_libraries(test_pair_list PRIVATE lammps GTest::GMockMain)
add_test(NAME TestPairList COMMAND test_pair_list)

100
unittest/force-styles/test_pair_list.cpp Normal file
View File

@ -0,0 +1,100 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "library.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
const char parms[] = "print \"\"\"\n"
"1 2 lj126 0.3 3.5 4.0\n"
"2 3 lj126 0.3 3.5 5.0\n"
"1 4 harmonic 10.0 7.0\n"
"2 4 harmonic 10.0 7.0\n"
"3 4 morse 10.0 0.3 6.5\n"
"\"\"\" file list.param\n";
const char first[] = "units real\n"
"atom_style bond\n"
"atom_modify map array\n"
"boundary f f f\n"
"special_bonds lj/coul 0.0 1.0 1.0\n"
"region box block -5 5 -5 5 -5 5\n"
"create_box 1 box bond/types 2 extra/bond/per/atom 4\n"
"create_atoms 1 single -2.0 0.0 0.0\n"
"create_atoms 1 single 0.0 1.0 0.0\n"
"create_atoms 1 single 4.0 1.0 0.0\n"
"create_atoms 1 single 4.0 -4.0 -4.0\n"
"create_bonds single/bond 1 1 4\n"
"create_bonds single/bond 1 2 4\n"
"create_bonds single/bond 2 3 4\n"
"mass 1 10.0\n"
"velocity all create 10.0 87287 loop geom\n";
const char second[] = "timestep 0.2\n"
"fix 1 all nve\n"
"run 2 post no\n";
static constexpr double EPSILON = 1.0e-10;
namespace LAMMPS_NS {
TEST(PairList, ListVsPairBond)
{
if (!lammps_config_has_package("MOLECULE")) GTEST_SKIP();
if (!lammps_config_has_package("MISC")) GTEST_SKIP();
const char *lmpargv[] = {"melt", "-log", "none", "-nocite"};
int lmpargc = sizeof(lmpargv) / sizeof(const char *);
::testing::internal::CaptureStdout();
void *ljmelt = lammps_open_no_mpi(lmpargc, (char **)lmpargv, nullptr);
lmpargv[0] = "plist";
void *plist = lammps_open_no_mpi(lmpargc, (char **)lmpargv, nullptr);
lammps_commands_string(ljmelt, first);
lammps_command(ljmelt, "pair_style lj/cut 5.0");
lammps_command(ljmelt, "pair_coeff * * 0.3 3.5");
lammps_command(ljmelt, "bond_style hybrid harmonic morse");
lammps_command(ljmelt, "bond_coeff 1 harmonic 10.0 7.0");
lammps_command(ljmelt, "bond_coeff 2 morse 10.0 0.3 6.5");
lammps_commands_string(ljmelt, second);
lammps_command(plist, parms);
lammps_commands_string(plist, first);
lammps_command(plist, "pair_style list list.param 10.0");
lammps_command(plist, "pair_coeff * *");
lammps_command(plist, "bond_style zero");
lammps_command(plist, "bond_coeff * 2.0");
lammps_commands_string(plist, second);
::testing::internal::GetCapturedStdout();
double lj_pe = lammps_get_thermo(ljmelt, "pe");
double ml_pe = lammps_get_thermo(plist, "pe");
EXPECT_NEAR(lj_pe, ml_pe, EPSILON);
double lj_ke = lammps_get_thermo(ljmelt, "ke");
double ml_ke = lammps_get_thermo(plist, "ke");
EXPECT_NEAR(lj_ke, ml_ke, EPSILON);
double lj_press = lammps_get_thermo(ljmelt, "press");
double ml_press = lammps_get_thermo(plist, "press");
EXPECT_NEAR(lj_press, ml_press, EPSILON);
::testing::internal::CaptureStdout();
lammps_command(plist, "shell rm list.param");
lammps_close(ljmelt);
lammps_close(plist);
::testing::internal::GetCapturedStdout();
}
} // namespace LAMMPS_NS

8
unittest/fortran/test_fortran_extract_variable.f90
View File

@ -33,8 +33,7 @@ CONTAINS
CHARACTER(LEN=256) :: test_input_directory
TYPE(c_ptr) :: c_test_input_directory, c_absolute_path, c_filename
CHARACTER(LEN=1,KIND=c_char), DIMENSION(:), POINTER :: F_absolute_path
INTEGER :: i
INTEGER(c_size_t) :: length
INTEGER(c_size_t) :: i, length
test_input_directory = lmp%extract_variable('input_dir')
c_test_input_directory = f2c_string(test_input_directory)
@ -91,7 +90,7 @@ FUNCTION f_lammps_with_C_args(argc, argv) BIND(C)
TYPE(c_ptr) :: f_lammps_with_C_args
CHARACTER(LEN=ARG_LENGTH), DIMENSION(argc) :: args
CHARACTER(LEN=1,KIND=c_char), DIMENSION(:), POINTER :: Cstr
INTEGER :: i, length, j
INTEGER(c_size_t):: i, length, j
INTERFACE
FUNCTION c_strlen(str) BIND(C,name='strlen')
@ -346,12 +345,11 @@ FUNCTION f_lammps_extract_variable_atomfile(i) BIND(C)
f_lammps_extract_variable_atomfile = atom_data(i)
END FUNCTION f_lammps_extract_variable_atomfile
FUNCTION f_lammps_extract_variable_python(i) BIND(C)
FUNCTION f_lammps_extract_variable_python() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double
USE LIBLAMMPS
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_variable_python
f_lammps_extract_variable_python = lmp%extract_variable('py')

1
unittest/fortran/test_fortran_gather_scatter.f90
View File

@ -190,7 +190,6 @@ SUBROUTINE f_lammps_scatter_atoms_subset_mask() BIND(C)
INTEGER(c_int), DIMENSION(:), ALLOCATABLE :: all_masks
INTEGER(c_int), DIMENSION(*), PARAMETER :: tags = [3,1]
INTEGER(c_int), DIMENSION(2) :: masks
INTEGER(c_int) :: swap
CALL lmp%gather_atoms('mask', 1_c_int, all_masks)

4
unittest/fortran/wrap_extract_variable.cpp
View File

@ -165,7 +165,7 @@ TEST_F(LAMMPS_extract_variable, format)
{
f_lammps_setup_extract_variable();
int i;
char str[10];
char str[16];
char *fstr;
for (i = 1; i <= 10; i++) {
std::sprintf(str, "%.6G", std::exp(i));
@ -180,7 +180,7 @@ TEST_F(LAMMPS_extract_variable, format_pad)
{
f_lammps_setup_extract_variable();
int i;
char str[10];
char str[16];
char *fstr;
for (i = 1; i <= 10; i++) {
std::sprintf(str, "%08.6G", std::exp(i));

69
unittest/python/python-commands.py
View File

@ -209,6 +209,75 @@ create_atoms 1 single &
self.assertEqual(idx,i)
self.assertEqual(num,nlocal-1)
def testNeighborListZeroHalf(self):
self.lmp.commands_string("""
boundary f f f
units real
region box block -5 5 -5 5 -5 5
create_box 1 box
mass 1 1.0
pair_style zero 4.0
pair_coeff 1 1
""")
x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
0.0, 0.0, 1.0 ]
tags = [1, 2, 3, 4, 5, 6, 7]
types = [1, 1, 1, 1, 1, 1, 1]
self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
nlocal = self.lmp.extract_global("nlocal")
self.assertEqual(nlocal, 7)
self.lmp.command("run 0 post no")
self.assertEqual(self.lmp.find_pair_neighlist("zero"),0)
nlist = self.lmp.get_neighlist(0)
self.assertEqual(nlist.size, 7)
for i in range(0,nlist.size):
idx, num, neighs = nlist.get(i)
self.assertEqual(idx,i)
self.assertEqual(num,nlocal-1-i)
# look up neighbor list by atom index
num, neighs = nlist.find(2)
self.assertEqual(num,4)
self.assertIsNotNone(neighs,None)
# this one will fail
num, neighs = nlist.find(10)
self.assertEqual(num,-1)
self.assertIsNone(neighs,None)
def testNeighborListZeroFull(self):
self.lmp.commands_string("""
boundary f f f
units metal
region box block -5 5 -5 5 -5 5
create_box 1 box
mass 1 1.0
pair_style zero 4.0 full
pair_coeff * *
""")
x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
0.0, 0.0, 1.0 ]
tags = [1, 2, 3, 4, 5, 6, 7]
types = [1, 1, 1, 1, 1, 1, 1]
self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
nlocal = self.lmp.extract_global("nlocal")
self.assertEqual(nlocal, 7)
self.lmp.command("run 0 post no")
self.assertEqual(self.lmp.find_pair_neighlist("zero"),0)
nlist = self.lmp.get_neighlist(0)
self.assertEqual(nlist.size, 7)
for i in range(0,nlist.size):
idx, num, neighs = nlist.get(i)
self.assertEqual(idx,i)
self.assertEqual(num,nlocal-1)
@unittest.skipIf(not has_manybody,"Hybrid neighbor list test for manybody potential")
def testNeighborListHybrid(self):
self.lmp.commands_string("""

68
unittest/python/python-numpy.py
View File

@ -412,6 +412,74 @@ class PythonNumpy(unittest.TestCase):
idx, neighs = nlist.get(i)
self.assertEqual(neighs.size,nlocal-1-i)
def testNeighborListZeroHalf(self):
self.lmp.commands_string("""
boundary f f f
units real
region box block -5 5 -5 5 -5 5
create_box 1 box
mass 1 1.0
pair_style zero 4.0
pair_coeff 1 1
""")
x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
0.0, 0.0, 1.0 ]
tags = [1, 2, 3, 4, 5, 6, 7]
types = [1, 1, 1, 1, 1, 1, 1]
self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
nlocal = self.lmp.extract_global("nlocal")
self.assertEqual(nlocal, 7)
self.lmp.command("run 0 post no")
self.assertEqual(self.lmp.find_pair_neighlist("zero"),0)
nlist = self.lmp.numpy.get_neighlist(0)
self.assertEqual(nlist.size, 7)
for i in range(0,nlist.size):
idx, neighs = nlist.get(i)
self.assertEqual(idx,i)
self.assertEqual(neighs.size,nlocal-1-i)
# look up neighbor list by atom index
neighs = nlist.find(2)
self.assertEqual(neighs.size,4)
self.assertIsNotNone(neighs,None)
# this one will fail
neighs = nlist.find(10)
self.assertIsNone(neighs,None)
def testNeighborListZeroFull(self):
self.lmp.commands_string("""
boundary f f f
units metal
region box block -5 5 -5 5 -5 5
create_box 1 box
mass 1 1.0
pair_style zero 4.0 full
pair_coeff * *
""")
x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
0.0, 0.0, 1.0 ]
tags = [1, 2, 3, 4, 5, 6, 7]
types = [1, 1, 1, 1, 1, 1, 1]
self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
nlocal = self.lmp.extract_global("nlocal")
self.assertEqual(nlocal, 7)
self.lmp.command("run 0 post no")
self.assertEqual(self.lmp.find_pair_neighlist("zero"),0)
nlist = self.lmp.numpy.get_neighlist(0)
self.assertEqual(nlist.size, 7)
for i in range(0,nlist.size):
idx, neighs = nlist.get(i)
self.assertEqual(idx,i)
self.assertEqual(neighs.size,nlocal-1)
def testNeighborListCompute(self):
self.lmp.commands_string("""
boundary f f f