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Merge branch 'master' into collected-small-changes

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This commit is contained in:
Axel Kohlmeyer
2021-02-16 12:16:14 -05:00
parent e7a37877c0 4fdc7a1362
commit 395f6f6107
7 changed files with 40 additions and 29 deletions
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6
cmake/Modules/Packages/KIM.cmake
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@ -69,14 +69,14 @@ if(DOWNLOAD_KIM)
BUILD_RPATH "${_rpath_prefix}/kim_build-prefix/lib"
)
else()
if(KIM-API_FOUND AND KIM_API_VERSION VERSION_GREATER_EQUAL 2.2.0)
if(KIM-API_FOUND AND KIM-API_VERSION VERSION_GREATER_EQUAL 2.2.0)
# For kim-api >= 2.2.0
find_package(KIM-API ${KIM-API_MIN_VERSION} CONFIG REQUIRED)
find_package(KIM-API 2.2.0 CONFIG REQUIRED)
target_link_libraries(lammps PRIVATE KIM-API::kim-api)
else()
# For kim-api 2.1.3 (consistent with previous version of this file)
find_package(PkgConfig REQUIRED)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=KIM-API_MIN_VERSION)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
endif()
endif()

2
doc/src/Python_atoms.rst
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@ -50,7 +50,7 @@ against invalid accesses.
**Numpy Methods**:
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
.. tab:: PyLammps/IPyLammps API

12
doc/src/Python_module.rst
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@ -61,7 +61,7 @@ functions. Below is a detailed documentation of the API.
.. autoclass:: lammps.lammps
:members:
.. autoclass:: lammps.numpy::numpy_wrapper
.. autoclass:: lammps.numpy_wrapper::numpy_wrapper
:members:
----------
@ -134,8 +134,8 @@ Style Constants
to request from computes or fixes. See :cpp:enum:`_LMP_STYLE_CONST`
for the equivalent constants in the C library interface. Used in
:py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
:py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
:py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
.. _py_type_constants:
@ -149,8 +149,8 @@ Type Constants
to request from computes or fixes. See :cpp:enum:`_LMP_TYPE_CONST`
for the equivalent constants in the C library interface. Used in
:py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
:py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
:py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
.. _py_vartype_constants:
@ -170,6 +170,6 @@ Classes representing internal objects
:members:
:no-undoc-members:
.. autoclass:: lammps.numpy::NumPyNeighList
.. autoclass:: lammps.numpy_wrapper::NumPyNeighList
:members:
:no-undoc-members:

4
doc/src/Python_neighbor.rst
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@ -14,5 +14,5 @@ Neighbor list access
**NumPy Methods:**
* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)
* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)

12
doc/src/Python_objects.rst
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@ -36,9 +36,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
Python subscripting. The values will be zero for atoms not in the
specified group.
:py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`,
:py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`, and
:py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>` are
:py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`,
:py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`, and
:py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>` are
equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers.
The :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>` method sets an
@ -54,9 +54,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
**NumPy Methods**:
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
.. tab:: PyLammps/IPyLammps API

2
python/lammps/core.py
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@ -1612,7 +1612,7 @@ class lammps(object):
def get_neighlist(self, idx):
"""Returns an instance of :class:`NeighList` which wraps access to the neighbor list with the given index
See :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.get_neighlist()>` if you want to use
See :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>` if you want to use
NumPy arrays instead of ``c_int`` pointers.
:param idx: index of neighbor list

31
src/USER-REACTION/fix_bond_react.cpp
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@ -1031,23 +1031,28 @@ void FixBondReact::post_integrate()
if (finalpartner[i] == 0) continue;
j = atom->map(finalpartner[i]);
// if (j < 0 || tag[i] < tag[j]) {
if (tag[i] < tag[j]) { //atom->map(std::min(tag[i],tag[j])) <= nlocal &&
if (nattempt[rxnID] == maxattempt) {
if (tag[i] < tag[j]) {
if (nattempt[rxnID] > maxattempt-2) {
maxattempt += DELTA;
// third column of 'attempt': bond/react integer ID
// third dim of 'attempt': bond/react integer ID
memory->grow(attempt,maxattempt,2,nreacts,"bond/react:attempt");
}
// to ensure types remain in same order
// unnecessary now taken from reaction map file
if (iatomtype[rxnID] == type[i]) {
attempt[nattempt[rxnID]][0][rxnID] = tag[i];
attempt[nattempt[rxnID]][1][rxnID] = finalpartner[i];
nattempt[rxnID]++;
// add another attempt if initiator atoms are same type
if (iatomtype[rxnID] == jatomtype[rxnID]) {
attempt[nattempt[rxnID]][0][rxnID] = finalpartner[i];
attempt[nattempt[rxnID]][1][rxnID] = tag[i];
nattempt[rxnID]++;
}
} else {
attempt[nattempt[rxnID]][0][rxnID] = finalpartner[i];
attempt[nattempt[rxnID]][1][rxnID] = tag[i];
nattempt[rxnID]++;
}
nattempt[rxnID]++;
}
}
}
@ -2705,7 +2710,7 @@ update molecule IDs, charges, types, special lists and all topology
void FixBondReact::update_everything()
{
int nlocal; // must be defined after create_atoms
int nlocal = atom->nlocal; // must be redefined after create atoms
int *type = atom->type;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
@ -2717,6 +2722,9 @@ void FixBondReact::update_everything()
// used when deleting atoms
int ndel,ndelone;
int *mark;
int nmark = nlocal;
memory->create(mark,nmark,"bond/react:mark");
for (int i = 0; i < nmark; i++) mark[i] = 0;
tagint *tag = atom->tag;
AtomVec *avec = atom->avec;
@ -2778,8 +2786,11 @@ void FixBondReact::update_everything()
// mark to-delete atoms
nlocal = atom->nlocal;
mark = new int[nlocal];
for (int i = 0; i < nlocal; i++) mark[i] = 0;
if (nlocal > nmark) {
memory->grow(mark,nlocal,"bond/react:mark");
for (int i = nmark; i < nlocal; i++) mark[i] = 0;
nmark = nlocal;
}
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
onemol = atom->molecules[unreacted_mol[rxnID]];
@ -3228,7 +3239,7 @@ void FixBondReact::update_everything()
}
}
}
delete [] mark;
memory->destroy(mark);
MPI_Allreduce(&ndelone,&ndel,1,MPI_INT,MPI_SUM,world);