ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #2854 from akohlmey/final-fixes-for-patch-release

Browse Source 
Final fixes for the patch release
This commit is contained in:
Axel Kohlmeyer
2021-07-27 20:31:52 -04:00
committed by GitHub
parent 8e6b7bf6e5 bb5da016d4
commit ed34856961
11 changed files with 59 additions and 34 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
cmake/CMakeLists.txt
View File

@ -312,6 +312,7 @@ pkg_depends(LATBOLTZ MPI)
pkg_depends(PHONON KSPACE)
pkg_depends(SCAFACOS MPI)
pkg_depends(DIELECTRIC KSPACE)
pkg_depends(DIELECTRIC EXTRA-PAIR)
pkg_depends(CG-DNA MOLECULE)
pkg_depends(CG-DNA ASPHERE)

25
doc/src/Packages_details.rst
View File

@ -189,6 +189,7 @@ atomic information to continuum fields.
**Install:**
This package has :ref:`specific installation instructions <atc>` on the :doc:`Build extras <Build_extras>` page.
The ATC package requires that also the `MANYBODY <PKG-MANYBODY>`_ package is installed.
**Supporting info:**
@ -518,6 +519,11 @@ compute for simulating systems using boundary element solvers for
computing the induced charges at the interface between two media with
different dielectric constants.
**Install:**
To use this package, also the :ref:`KSPACE <PKG-KSPACE>` and
:ref:`EXTRA-PAIR <PKG-EXTRA-PAIR>` packages need to be installed.
**Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U)
**Supporting info:**
@ -1210,6 +1216,10 @@ can be used to model MD particles influenced by hydrodynamic forces.
**Authors:** Frances Mackay and Colin Denniston (University of Western
Ontario).
**Install:**
The LATBOLTZ package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
**Supporting info:**
* src/LATBOLTZ: filenames -> commands
@ -1603,9 +1613,9 @@ A general interface for machine-learning interatomic potentials, including PyTor
**Install:**
To use this package, also the :ref:`ML-SNAP package <PKG-ML-SNAP>` package needs
To use this package, also the :ref:`ML-SNAP <PKG-ML-SNAP>` package needs
to be installed. To make the *mliappy* model available, also the
:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed, the version
:ref:`PYTHON <PKG-PYTHON>` package needs to be installed, the version
of Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
must be installed.
@ -1870,6 +1880,10 @@ MPIIO library. It adds :doc:`dump styles <dump>` with a "mpiio" in
their style name. Restart files with an ".mpiio" suffix are also
written and read in parallel.
**Install:**
The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
**Supporting info:**
* src/MPIIO: filenames -> commands
@ -2103,6 +2117,12 @@ And a :doc:`dynamical_matrix <dynamical_matrix>` as well as a
:doc:`third_order <third_order>` command to compute the dynamical matrix
and third order tensor from finite differences.
**Install:**
The PHONON package requires that also the `KSPACE <PKG-KSPACE>`_
package is installed.
**Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
@ -2486,6 +2506,7 @@ the Forschungszentrum Juelich.
**Install:**
This package has :ref:`specific installation instructions <scafacos>` on the :doc:`Build extras <Build_extras>` page.
The SCAFACOS package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
**Supporting info:**

3
doc/src/fix_nve_noforce.rst
View File

@ -49,8 +49,7 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
none
Related commands
""""""""""""""""

4
src/DIELECTRIC/Install.sh
View File

@ -34,6 +34,10 @@ if (test $1 = 1) then
echo "Must install KSPACE package with DIELECTRIC package"
exit 1
fi
if (test ! -e ../pair_lj_cut_coul_debye.cpp) then
echo "Must install EXTRA-PAIR package with DIELECTRIC package"
exit 1
fi
fi
for file in *.cpp *.h; do

4
src/INTEL/intel_intrinsics_airebo.h
View File

@ -623,7 +623,7 @@ public:
) {
assert(scale == sizeof(FVEC_SCAL_T));
# if FVEC_LEN==8
FVEC_SUFFIX(_mm512_mask_i32scatter_)(mem, mask.val_,
FVEC_SUFFIX(_mm512_mask_i32scatter_)(mem, mask.val_,
_mm512_castsi512_si256(idx.val_),
a.val_, sizeof(FVEC_SCAL_T));
# else
@ -668,7 +668,7 @@ public:
const double * mem, const int scale
) {
assert(scale == sizeof(double));
__m512d lo = _mm512_mask_i32gather_pd(src.lo_, mask.val_,
__m512d lo = _mm512_mask_i32gather_pd(src.lo_, mask.val_,
_mm512_castsi512_si256(idx.val_),
mem, sizeof(double));
__m512d hi = _mm512_mask_i32gather_pd(src.hi_, get_bvec_hi(mask.val_),

2
src/INTEL/intel_preprocess.h
View File

@ -338,7 +338,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
#endif
// TO BE DEPRECATED
#ifndef USE_OMP_SIMD
#ifndef USE_OMP_SIMD
#define IP_PRE_fdotr_acc_force_l5(lf, lt, minlocal, nthreads, f_start, \
f_stride, pos, ov0, ov1, ov2, \

36
src/INTEL/intel_simd.h
View File

@ -838,10 +838,10 @@ namespace ip_simd {
x = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), atom,
_MM_SCALE_2);
y = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
y = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), atom+1,
_MM_SCALE_2);
z = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
z = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), atom+2,
_MM_SCALE_2);
}
@ -852,10 +852,10 @@ namespace ip_simd {
x = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), atom,
_MM_SCALE_2);
y = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
y = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), atom+1,
_MM_SCALE_2);
z = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
z = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), atom+2,
_MM_SCALE_2);
type = _mm512_mask_i32gather_epi32(_mm512_undefined_epi32(), m, i, atom+3,
@ -895,7 +895,7 @@ namespace ip_simd {
const SIMD_int &joffset, SIMD_double &eng) {
SIMD_double jeng;
SIMD_conflict_pi_reduce1(rmask, joffset, eng);
jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
_mm512_castsi512_si256(joffset),
force, _MM_SCALE_2);
jeng = jeng + eng;
@ -908,7 +908,7 @@ namespace ip_simd {
SIMD_double engd, jeng;
engd = _mm512_cvtps_pd(_mm512_castps512_ps256(eng));
SIMD_conflict_pi_reduce1(rmask, joffset, engd);
jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
_mm512_castsi512_si256(joffset),
force, _MM_SCALE_2);
jeng = jeng + engd;
@ -920,7 +920,7 @@ namespace ip_simd {
_mm512_shuffle_f32x4(eng,eng,238)));
SIMD_int joffset2 = _mm512_shuffle_i32x4(joffset, joffset, 238);
SIMD_conflict_pi_reduce1(rmask2, joffset2, engd);
jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2,
jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2,
_mm512_castsi512_si256(joffset2),
force, _MM_SCALE_2);
jeng = jeng + engd;
@ -939,7 +939,7 @@ namespace ip_simd {
SIMD_double jeng;
SIMD_conflict_pi_reduce1(rmask, joffset, eng);
jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
jeng = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
_mm512_castsi512_si256(joffset),
force, _MM_SCALE_2);
jeng = jeng + eng;
@ -971,7 +971,7 @@ namespace ip_simd {
SIMD_double &fy, SIMD_double &fz) {
SIMD_conflict_pi_reduce3(m, i, fx, fy, fz);
SIMD_double jfrc;
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), force,
_MM_SCALE_2);
jfrc = jfrc + fx;
@ -983,7 +983,7 @@ namespace ip_simd {
jfrc = jfrc + fy;
_mm512_mask_i32scatter_pd(force+1, m, _mm512_castsi512_si256(i), jfrc,
_MM_SCALE_2);
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), force + 2,
_MM_SCALE_2);
jfrc = jfrc + fz;
@ -1000,13 +1000,13 @@ namespace ip_simd {
amzd = _mm512_cvtps_pd(_mm512_castps512_ps256(amz));
SIMD_conflict_pi_reduce3(rmask, joffset, amxd, amyd, amzd);
SIMD_double jfrc;
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
_mm512_castsi512_si256(joffset),
force, _MM_SCALE_2);
jfrc = jfrc + amxd;
_mm512_mask_i32scatter_pd(force, rmask, _mm512_castsi512_si256(joffset),
jfrc, _MM_SCALE_2);
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask,
_mm512_castsi512_si256(joffset),
force + 1, _MM_SCALE_2);
jfrc = jfrc + amyd;
@ -1028,13 +1028,13 @@ namespace ip_simd {
_mm512_shuffle_f32x4(amz,amz,238)));
SIMD_int joffset2 = _mm512_shuffle_i32x4(joffset, joffset, 238);
SIMD_conflict_pi_reduce3(rmask2, joffset2, amxd, amyd, amzd);
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2,
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2,
_mm512_castsi512_si256(joffset2),
force, _MM_SCALE_2);
jfrc = jfrc + amxd;
_mm512_mask_i32scatter_pd(force, rmask2, _mm512_castsi512_si256(joffset2),
jfrc, _MM_SCALE_2);
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2,
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), rmask2,
_mm512_castsi512_si256(joffset2),
force + 1, _MM_SCALE_2);
jfrc = jfrc + amyd;
@ -1045,7 +1045,7 @@ namespace ip_simd {
_mm512_castsi512_si256(joffset2),
force + 2, _MM_SCALE_2);
jfrc = jfrc + amzd;
_mm512_mask_i32scatter_pd(force+2, rmask2,
_mm512_mask_i32scatter_pd(force+2, rmask2,
_mm512_castsi512_si256(joffset2), jfrc,
_MM_SCALE_2);
}
@ -1099,7 +1099,7 @@ namespace ip_simd {
const SIMD_int &i, const SIMD_double &fx,
const SIMD_double &fy, const SIMD_double &fz) {
SIMD_double jfrc;
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), force,
_MM_SCALE_2);
jfrc = jfrc - fx;
@ -1866,7 +1866,7 @@ namespace ip_simd {
jfrc = jfrc + fx;
_mm512_mask_i32scatter_pd(force, m, _mm512_castsi512_si256(i), jfrc,
_MM_SCALE_2);
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i), force + 1,
_MM_SCALE_2);
jfrc = jfrc + fy;
@ -1880,7 +1880,7 @@ namespace ip_simd {
_MM_SCALE_2);
if (EFLAG) {
if (eatom) {
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
jfrc = _mm512_mask_i32gather_pd(_mm512_undefined_pd(), m,
_mm512_castsi512_si256(i),
force + 3, _MM_SCALE_2);
jfrc = jfrc + fwtmp;

2
src/INTEL/pair_buck_intel.cpp
View File

@ -231,7 +231,7 @@ void PairBuckIntel::eval(const int offload, const int vflag,
fxtmp = fytmp = fztmp = (acc_t)0;
if (EFLAG) fwtmp = sevdwl = (acc_t)0;
if (NEWTON_PAIR == 0)
if (vflag == VIRIAL_PAIR)
if (vflag == VIRIAL_PAIR)
sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0;
#if defined(LMP_SIMD_COMPILER)

16
src/KOKKOS/Install.sh
View File

@ -251,20 +251,20 @@ action pair_lj_class2_kokkos.cpp pair_lj_class2.cpp
action pair_lj_class2_kokkos.h pair_lj_class2.h
action pair_lj_cut_coul_cut_kokkos.cpp
action pair_lj_cut_coul_cut_kokkos.h
action pair_lj_cut_coul_debye_kokkos.cpp
action pair_lj_cut_coul_debye_kokkos.h
action pair_lj_cut_coul_dsf_kokkos.cpp
action pair_lj_cut_coul_dsf_kokkos.h
action pair_lj_cut_coul_debye_kokkos.cpp pair_lj_cut_coul_debye.cpp
action pair_lj_cut_coul_debye_kokkos.h pair_lj_cut_coul_debye.h
action pair_lj_cut_coul_dsf_kokkos.cpp pair_lj_cut_coul_dsf.cpp
action pair_lj_cut_coul_dsf_kokkos.h pair_lj_cut_coul_dsf.h
action pair_lj_cut_coul_long_kokkos.cpp pair_lj_cut_coul_long.cpp
action pair_lj_cut_coul_long_kokkos.h pair_lj_cut_coul_long.h
action pair_lj_cut_kokkos.cpp
action pair_lj_cut_kokkos.h
action pair_lj_expand_kokkos.cpp
action pair_lj_expand_kokkos.h
action pair_lj_gromacs_coul_gromacs_kokkos.cpp
action pair_lj_gromacs_coul_gromacs_kokkos.h
action pair_lj_gromacs_kokkos.cpp
action pair_lj_gromacs_kokkos.h
action pair_lj_gromacs_coul_gromacs_kokkos.cpp pair_lj_gromacs_coul_gromacs.cpp
action pair_lj_gromacs_coul_gromacs_kokkos.h pair_lj_gromacs_coul_gromacs.h
action pair_lj_gromacs_kokkos.cpp pair_lj_gromacs.cpp
action pair_lj_gromacs_kokkos.h pair_lj_gromacs.h
action pair_lj_sdk_kokkos.cpp pair_lj_sdk.cpp
action pair_lj_sdk_kokkos.h pair_lj_sdk.h
action pair_morse_kokkos.cpp

0
src/EXTRA-FIX/fix_nve_noforce.cpp → src/fix_nve_noforce.cpp
View File

0
src/EXTRA-FIX/fix_nve_noforce.h → src/fix_nve_noforce.h
View File