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Merge pull request #1923 from akohlmey/collected_small_fixes 

Collected small fixes for the next patch
This commit is contained in:
Axel Kohlmeyer 2020-03-10 19:38:40 -04:00 committed by GitHub
parent b9ff623c16 e9f5b8246a
commit 33996d9bac
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GPG Key ID: 4AEE18F83AFDEB23
10 changed files with 46 additions and 52 deletions
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6
cmake/presets/all_off.cmake
View File

@ -7,11 +7,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

6
cmake/presets/all_on.cmake
View File

@ -9,11 +9,11 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

14
cmake/presets/most.cmake
View File

@ -2,13 +2,13 @@
# external libraries. Compared to all_on.cmake some more unusual packages
# are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
USER-DRUDE USER-FEP USER-MEAMC USER-MESO
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
USER-SPH USER-SMD USER-UEF USER-YAFF)
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

10
doc/src/pair_dpd.rst
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@ -129,13 +129,17 @@ the work of :ref:`(Afshar) <Afshar>` and :ref:`(Phillips) <Phillips>`.
.. note::
The virial calculation for pressure when using this pair style
The virial calculation for pressure when using these pair styles
includes all the components of force listed above, including the
random force.
random force. Since the random force depends on random numbers,
everything that changes the order of atoms in the neighbor list
(e.g. different number of MPI ranks or a different neighbor list
skin distance) will also change the sequence in which the random
numbers are applied and thus the individual forces and therefore
also the virial/pressure.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available

12
doc/src/pair_srp.rst
View File

@ -15,9 +15,9 @@ Syntax
* distance = *min* or *mid*
* zero or more keyword/value pairs may be appended
* keyword = *exclude*
.. parsed-literal::
*bptype* value = atom type for bond particles
*exclude* value = *yes* or *no*
@ -34,7 +34,7 @@ Examples
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 \* min exclude yes
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0
@ -60,7 +60,7 @@ bond-pairwise potential, such that the force on bond *i* due to bond
.. math::
F^{SRP}_{ij} & = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c
F^{\mathrm{SRP}}_{ij} = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c
where *r* and :math:`\hat{r}_{ij}` are the distance and unit vector
@ -74,8 +74,8 @@ lever rule,
.. math::
F_{i1}^{SRP} & = F^{SRP}_{ij}(L) \\
F_{i2}^{SRP} & = F^{SRP}_{ij}(1-L)
F_{i1}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(L) \\
F_{i2}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(1-L)
where *L* is the normalized distance from the atom to the point of

5
python/lammps.py
View File

@ -486,6 +486,7 @@ class lammps(object):
return None
elif style == 2:
self.lib.lammps_extract_compute.restype = POINTER(c_int)
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr[0]
if type == 1:
self.lib.lammps_extract_compute.restype = POINTER(c_double)
@ -509,6 +510,10 @@ class lammps(object):
result = ptr[0]
self.lib.lammps_free(ptr)
return result
elif (style == 2) and (type == 0):
self.lib.lammps_extract_fix.restype = POINTER(c_int)
ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
return ptr[0]
elif (style == 1) or (style == 2):
if type == 1:
self.lib.lammps_extract_fix.restype = POINTER(c_double)

2
src/KOKKOS/pair_snap_kokkos.h
View File

@ -38,7 +38,7 @@ struct TagPairSNAPComputeNeigh{};
struct TagPairSNAPPreUi{};
struct TagPairSNAPComputeUi{};
struct TagPairSNAPComputeUiTot{}; // accumulate ulist into ulisttot separately
struct TagPairSNAPComputeUiCPU{};
struct TagPairSNAPComputeUiCPU{};
struct TagPairSNAPComputeZi{};
struct TagPairSNAPComputeBi{};
struct TagPairSNAPZeroYi{};

6
src/KOKKOS/sna_kokkos.h
View File

@ -32,7 +32,7 @@ template <typename real>
struct alignas(2*sizeof(real)) SNAComplex
{
real re,im;
KOKKOS_FORCEINLINE_FUNCTION SNAComplex() = default;
KOKKOS_FORCEINLINE_FUNCTION SNAComplex(real re)
@ -172,7 +172,7 @@ inline
static KOKKOS_FORCEINLINE_FUNCTION
void caxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y);
// efficient complex FMA, conjugate of scalar
// efficient complex FMA, conjugate of scalar
static KOKKOS_FORCEINLINE_FUNCTION
void caconjxpy(const SNAcomplex& a, const SNAcomplex& x, SNAcomplex& y);
@ -201,7 +201,7 @@ inline
void grow_rij(int, int);
int twojmax, diagonalstyle;
t_sna_2d_ll blist;
t_sna_2c_ll ulisttot;
t_sna_2c_ll zlist;

35
src/library.cpp
View File

@ -537,35 +537,19 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
if (style == 1) {
if (!compute->peratom_flag) return NULL;
if (type == 1) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->vector_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->array_atom;
}
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
if (type == 1) return (void *) compute->vector_atom;
if (type == 2) return (void *) compute->array_atom;
}
if (style == 2) {
if (!compute->local_flag) return NULL;
if (type == 0) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) &compute->size_local_rows;
}
if (type == 1) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->vector_local;
}
if (type == 2) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->array_local;
}
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
if (type == 0) return (void *) &compute->size_local_rows;
if (type == 1) return (void *) compute->vector_local;
if (type == 2) return (void *) compute->array_local;
}
}
END_CAPTURE
@ -637,6 +621,7 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
if (style == 2) {
if (!fix->local_flag) return NULL;
if (type == 0) return (void *) &fix->size_local_rows;
if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local;
}

2
src/min_cg.cpp
View File

@ -113,7 +113,7 @@ int MinCG::iterate(int maxiter)
if (update->ftol > 0.0) {
if (normstyle == MAX) fdotf = fnorm_max(); // max force norm
else if (normstyle == INF) fdotf = fnorm_inf(); // infinite force norm
else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm
else if (normstyle == TWO) fdotf = dotall[0]; // same as fnorm_sqr(), Euclidean force 2-norm
else error->all(FLERR,"Illegal min_modify command");
if (fdotf < update->ftol*update->ftol) return FTOL;
}