jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #1197 from akohlmey/collected-small-fixes 

Collection of small changes and bugfixes for the next release
This commit is contained in:
Axel Kohlmeyer 2018-11-13 15:18:09 -05:00 committed by GitHub
parent b1186a971e 5a4e44b75a
commit 2c644c5f2e
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
13 changed files with 33 additions and 17 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
cmake/presets/all_off.cmake
View File

@ -13,7 +13,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})

2
cmake/presets/all_on.cmake
View File

@ -13,7 +13,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})

3
cmake/presets/manual_selection.cmake
View File

@ -56,7 +56,8 @@ set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE)
set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE)
set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE)
set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)

2
cmake/presets/nolib.cmake
View File

@ -13,7 +13,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})

2
cmake/presets/user.cmake
View File

@ -13,7 +13,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})

6
doc/src/Build_basics.txt
View File

@ -137,9 +137,9 @@ simply loading the appropriate module before building LAMMPS.
-D CMAKE_C_COMPILER=name # name of C compiler
-D CMAKE_Fortran_COMPILER=name # name of Fortran compiler :pre
-D CMAKE_CXX_FlAGS=string # flags to use with C++ compiler
-D CMAKE_C_FlAGS=string # flags to use with C compiler
-D CMAKE_Fortran_FlAGS=string # flags to use with Fortran compiler :pre
-D CMAKE_CXX_FLAGS=string # flags to use with C++ compiler
-D CMAKE_C_FLAGS=string # flags to use with C compiler
-D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler :pre
By default CMake will use a compiler it finds and it will add
optimization flags appropriate to that compiler and any "accelerator

2
doc/src/compute_ptm_atom.txt
View File

@ -117,5 +117,5 @@ package"_Build_package.html doc page for more info.
:line
:link(Larsen)
[(Larsen)] Larsen, Schmidt, Schiøtz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
[(Larsen)] Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).

2
doc/src/fix_bond_react.txt
View File

@ -41,7 +41,7 @@ react = mandatory argument indicating new reaction specification :l
fraction = initiate reaction with this probability if otherwise eligible
seed = random number seed (positive integer)
{stabilize_steps} value = timesteps
timesteps = number of timesteps to apply internally created nve/limit.html
timesteps = number of timesteps to apply internally created nve/limit fix :pre
{update_edges} value = {none} or {charges} :l
none = do not update topology near the edges of reaction templates
charges = update atomic charges of all atoms in reaction templates

6
src/USER-VTK/dump_vtk.cpp
View File

@ -93,10 +93,10 @@ enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats
#define ONEFIELD 32
#define DELTA 1048576
#if VTK_MAJOR_VERSION >= 7
#define InsertNextTupleValue InsertNextTypedTuple
#elif VTK_MAJOR_VERSION > 8
#if (VTK_MAJOR_VERSION < 5) || (VTK_MAJOR_VERSION > 8)
#error This code has only been tested with VTK 5, 6, 7, and 8
#elif VTK_MAJOR_VERSION > 6
#define InsertNextTupleValue InsertNextTypedTuple
#endif
/* ---------------------------------------------------------------------- */

17
src/bond_hybrid.cpp
View File

@ -33,6 +33,7 @@ BondHybrid::BondHybrid(LAMMPS *lmp) : Bond(lmp)
{
writedata = 0;
nstyles = 0;
has_quartic = -1;
}
/* ---------------------------------------------------------------------- */
@ -171,6 +172,7 @@ void BondHybrid::settings(int narg, char **arg)
delete [] styles;
for (int i = 0; i < nstyles; i++) delete [] keywords[i];
delete [] keywords;
has_quartic = -1;
}
if (allocated) {
@ -214,14 +216,23 @@ void BondHybrid::settings(int narg, char **arg)
i = 0;
while (i < narg) {
for (m = 0; m < nstyles; m++)
if (strcmp(arg[i],keywords[m]) == 0)
error->all(FLERR,"Bond style hybrid cannot use same bond style twice");
if (strcmp(arg[i],"hybrid") == 0)
error->all(FLERR,"Bond style hybrid cannot have hybrid as an argument");
if (strcmp(arg[i],"none") == 0)
error->all(FLERR,"Bond style hybrid cannot have none as an argument");
// register index of quartic bond type,
// so that bond type 0 can be mapped to it
if (strncmp(arg[i],"quartic",7) == 0)
has_quartic = m;
styles[nstyles] = force->new_bond(arg[i],1,dummy);
force->store_style(keywords[nstyles],arg[i],0);
@ -283,6 +294,12 @@ void BondHybrid::init_style()
{
for (int m = 0; m < nstyles; m++)
if (styles[m]) styles[m]->init_style();
// bond style quartic will set broken bonds to bond type 0, so we need
// to create an entry for it in the bond type to sub-style map
if (has_quartic >= 0)
map[0] = has_quartic;
}
/* ----------------------------------------------------------------------

2
src/bond_hybrid.h
View File

@ -47,7 +47,7 @@ class BondHybrid : public Bond {
private:
int *map; // which style each bond type points to
int has_quartic; // which style, if any is a quartic bond style
int *nbondlist; // # of bonds in sub-style bondlists
int *maxbond; // max # of bonds sub-style lists can store
int ***bondlist; // bondlist for each sub-style

2
tools/msi2lmp/src/MakeLists.c
View File

@ -363,7 +363,7 @@ int count_dihedrals()
if (i != k) {
for (ll=0; ll < atoms[k].no_connect; ll++) {
l = atoms[k].conn_no[ll];
if ((l != j) && (i != l)) n++
if ((l != j) && (i != l)) n++;
}
}
}

2
tools/msi2lmp/src/ReadCarFile.c
View File

@ -77,7 +77,6 @@ void ReadCarFile(void)
double cos_gamma;
double sin_gamma;
double cos_beta;
double sin_beta;
double A, B, C;
double center[3];
double hmat[6];
@ -265,7 +264,6 @@ void ReadCarFile(void)
cos_gamma = cos(pbc[5]*PI_180);
sin_gamma = sin(pbc[5]*PI_180);
cos_beta = cos(pbc[4]*PI_180);
sin_beta = sin(pbc[4]*PI_180);
if (pflag > 2) {
printf(" pbc[3] %f pbc[4] %f pbc[5] %f\n", pbc[3] ,pbc[4] ,pbc[5]);
printf(" cos_alpha %f cos_beta %f cos_gamma %f\n", cos_alpha ,cos_beta ,cos_gamma);