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Merge branch 'master' into doc-adjust3

This commit is contained in:
Axel Kohlmeyer 2018-11-26 14:47:29 -05:00
parent 79b3e9e27d 4004b8f161
commit c42d07d907
48 changed files with 2828 additions and 2747 deletions
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1
doc/Makefile
View File

@ -176,7 +176,6 @@ $(VENV):
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \
pip install Sphinx; \
pip install sphinxcontrib-images; \
deactivate;\
)

7
doc/github-development-workflow.md
View File

@ -55,11 +55,11 @@ required changes or ask the submitter of the pull request to implement
them. Even though, all LAMMPS developers may have write access to pull
requests (if enabled by the submitter, which is the default), only the
submitter or the assignee of a pull request may do so. During this
period the "work_in_progress" label shall be applied to the pull
period the `work_in_progress` label shall be applied to the pull
request. The assignee gets to decide what happens to the pull request
next, e.g. whether it should be assigned to a different developer for
additional checks and changes, or is recommended to be merged. Removing
the "work_in_progress" label and assigning the pull request to the
the `work_in_progress` label and assigning the pull request to the
developer tasked with merging signals that a pull request is ready to be
merged.
@ -145,6 +145,9 @@ Here are some items to check:
compiling LAMMPS with `-DLAMMPS_BIGBIG`.
* when including both `lmptype.h` (and using defines or macros from it)
and `mpi.h`, `lmptype.h` must be included first.
* when pair styles are added, check if settings for flags like
`single_enable`, `writedata`, `reinitflag`, `manybody_flag`
and others are correctly set and supported.
## GitHub Issues

5
doc/src/balance.txt
View File

@ -510,10 +510,13 @@ each processor, instead of 4, and "SQUARES" replaced by "CUBES".
For 2d simulations, the {z} style cannot be used. Nor can a "z"
appear in {dimstr} for the {shift} style.
Balancing through recursive bisectioning ({rcb} style) requires
"comm_style tiled"_comm_style.html
[Related commands:]
"group"_group.html, "processors"_processors.html,
"fix balance"_fix_balance.html
"fix balance"_fix_balance.html, "comm_style"_comm_style.html
[Default:] none
:link(pizza,http://pizza.sandia.gov)

5
doc/src/comm_style.txt
View File

@ -51,7 +51,10 @@ decomposition will be the same, as described by
commands. The decomposition can be changed via the
"balance"_balance.html or "fix balance"_fix_balance.html commands.
[Restrictions:] none
[Restrictions:]
Communication style {tiled} cannot be used with {triclinic} simulation
cells.
[Related commands:]

6
doc/src/fix_balance.txt
View File

@ -371,9 +371,13 @@ minimization"_minimize.html.
For 2d simulations, the {z} style cannot be used. Nor can a "z"
appear in {dimstr} for the {shift} style.
Balancing through recursive bisectioning ({rcb} style) requires
"comm_style tiled"_comm_style.html
[Related commands:]
"group"_group.html, "processors"_processors.html, "balance"_balance.html
"group"_group.html, "processors"_processors.html, "balance"_balance.html,
"comm_style"_comm_style.html
[Default:] none
:link(pizza,http://pizza.sandia.gov)

16
doc/src/special_bonds.txt
View File

@ -196,19 +196,25 @@ the options you need each time. This command cannot be used a 2nd
time incrementally. E.g. these two commands:
special_bonds lj 0.0 1.0 1.0
special_bonds coul 0.0 0.0 1.0
special_bonds coul 0.0 0.0 1.0 :pre
are not the same as
special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0
special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0 :pre
In the first case you end up with (after the 2nd command):
LJ: 0.0 0.0 0.0
Coul: coul 0.0 0.0 1.0
Coul: 0.0 0.0 1.0 :pre
because the LJ settings are reset to their default values
each time the command is issued.
while only in the second case, you get the desired settings of:
LJ: 0.0 1.0 1.0
Coul: 0.0 0.0 1.0 :pre
This happens because the LJ (and Coul) settings are reset to
their default values before modifying them, each time the
{special_bonds} command is issued.
[Restrictions:] none

2
doc/utils/sphinx-config/conf.py
View File

@ -248,7 +248,7 @@ latex_documents = [
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('Manual', 'liggghts', 'LAMMPS Documentation',
('Manual', 'lammps', 'LAMMPS Documentation',
['Steve Plimpton'], 1)
]

0
examples/USER/awpmd/H/README → examples/USER/awpmd/README
View File

0
examples/USER/awpmd/H/data.h_atom → examples/USER/awpmd/data.h_atom
View File

0
examples/USER/awpmd/H/data.h_molecule → examples/USER/awpmd/data.h_molecule
View File

0
examples/USER/awpmd/H/in.h_atom → examples/USER/awpmd/in.h_atom
View File

0
examples/USER/awpmd/H/in.h_molecule → examples/USER/awpmd/in.h_molecule
View File

12
lib/message/cslib/src/msg.cpp
View File

@ -13,9 +13,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <cstdio>
#include <cstring>
#include <cstdlib>
#include "msg.h"
@ -23,7 +23,7 @@ using namespace CSLIB_NS;
/* ---------------------------------------------------------------------- */
Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld)
Msg::Msg(int csflag, const void * /* ptr */, MPI_Comm cworld)
{
world = cworld;
MPI_Comm_rank(world,&me);
@ -34,7 +34,7 @@ Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld)
/* ---------------------------------------------------------------------- */
Msg::Msg(int csflag, const void *ptr)
Msg::Msg(int csflag, const void * /* ptr */)
{
world = 0;
me = 0;
@ -57,7 +57,7 @@ void Msg::init(int csflag)
/* ---------------------------------------------------------------------- */
void Msg::allocate(int nheader, int &maxheader, int *&header,
int nbuf, int &maxbuf, char *&buf)
int nbuf, int &maxbuf, char *&buf)
{
if (nheader > maxheader) {
sfree(header);

12
src/STUBS/mpi.c
View File

@ -463,8 +463,8 @@ int MPI_Allreduce(void *sendbuf, void *recvbuf, int count,
/* copy values from data1 to data2 */
int MPI_Reduce(void *sendbuf, void *recvbuf, int count,
MPI_Datatype datatype, MPI_Op op,
int root, MPI_Comm comm)
MPI_Datatype datatype, MPI_Op op,
int root, MPI_Comm comm)
{
int n = count * stubtypesize(datatype);
@ -550,8 +550,8 @@ int MPI_Gather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
/* copy values from data1 to data2 */
int MPI_Gatherv(void *sendbuf, int sendcount, MPI_Datatype sendtype,
void *recvbuf, int *recvcounts, int *displs,
MPI_Datatype recvtype, int root, MPI_Comm comm)
void *recvbuf, int *recvcounts, int *displs,
MPI_Datatype recvtype, int root, MPI_Comm comm)
{
int n = sendcount * stubtypesize(sendtype);
@ -581,8 +581,8 @@ int MPI_Scatter(void *sendbuf, int sendcount, MPI_Datatype sendtype,
/* copy values from data1 to data2 */
int MPI_Scatterv(void *sendbuf, int *sendcounts, int *displs,
MPI_Datatype sendtype, void *recvbuf, int recvcount,
MPI_Datatype recvtype, int root, MPI_Comm comm)
MPI_Datatype sendtype, void *recvbuf, int recvcount,
MPI_Datatype recvtype, int root, MPI_Comm comm)
{
int n = recvcount * stubtypesize(recvtype);

1
src/USER-MISC/pair_ilp_graphene_hbn.cpp
View File

@ -46,7 +46,6 @@ using namespace LAMMPS_NS;
PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
restartinfo = 0;
// initialize element to parameter maps

2
src/USER-MISC/pair_kolmogorov_crespi_full.cpp
View File

@ -46,8 +46,6 @@ using namespace LAMMPS_NS;
PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
// initialize element to parameter maps
nelements = 0;
elements = NULL;

2
src/USER-MISC/pair_kolmogorov_crespi_z.cpp
View File

@ -42,7 +42,7 @@ using namespace LAMMPS_NS;
PairKolmogorovCrespiZ::PairKolmogorovCrespiZ(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
single_enable = 0;
restartinfo = 0;
// initialize element to parameter maps

1
src/USER-MISC/pair_srp.cpp
View File

@ -68,6 +68,7 @@ static int srp_instance = 0;
PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
single_enable = 0;
if (lmp->citeme) lmp->citeme->add(cite_srp);

2
src/USER-OMP/pair_reaxc_omp.cpp
View File

@ -582,7 +582,7 @@ int PairReaxCOMP::write_reax_lists()
/* ---------------------------------------------------------------------- */
void PairReaxCOMP::read_reax_forces(int vflag)
void PairReaxCOMP::read_reax_forces(int /* vflag */)
{
#if defined(_OPENMP)
#pragma omp parallel for schedule(static) default(shared)

11
src/USER-OMP/reaxc_bond_orders_omp.cpp
View File

@ -220,7 +220,8 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj,
/* ---------------------------------------------------------------------- */
void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_data *data,
void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj,
simulation_data * /* data */,
storage *workspace, reax_list **lists ) {
reax_list *bonds = (*lists) + BONDS;
bond_data *nbr_j, *nbr_k;
@ -343,9 +344,9 @@ void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_
/* ---------------------------------------------------------------------- */
int BOp_OMP( storage *workspace, reax_list *bonds, double bo_cut,
int BOp_OMP( storage * /* workspace */, reax_list *bonds, double bo_cut,
int i, int btop_i, far_neighbor_data *nbr_pj,
single_body_parameters *sbp_i, single_body_parameters *sbp_j,
single_body_parameters * /* sbp_i */, single_body_parameters * /* sbp_j */,
two_body_parameters *twbp,
int btop_j, double C12, double C34, double C56, double BO, double BO_s, double BO_pi, double BO_pi2) {
int j;
@ -419,8 +420,8 @@ int BOp_OMP( storage *workspace, reax_list *bonds, double bo_cut,
/* ---------------------------------------------------------------------- */
void BOOMP( reax_system *system, control_params *control, simulation_data *data,
storage *workspace, reax_list **lists, output_controls *out_control )
void BOOMP( reax_system *system, control_params * /* control */, simulation_data * /* data */,
storage *workspace, reax_list **lists, output_controls * /* out_control */)
{
#ifdef OMP_TIMING
double endTimeBase, startTimeBase;

4
src/USER-OMP/reaxc_bonds_omp.cpp
View File

@ -42,9 +42,9 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void BondsOMP( reax_system *system, control_params *control,
void BondsOMP( reax_system *system, control_params * /* control */,
simulation_data *data, storage *workspace, reax_list **lists,
output_controls *out_control )
output_controls * /* out_control */)
{
#ifdef OMP_TIMING
double endTimeBase, startTimeBase;

10
src/USER-OMP/reaxc_forces_omp.cpp
View File

@ -79,7 +79,7 @@ void Init_Force_FunctionsOMP( control_params *control )
void Compute_Bonded_ForcesOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
MPI_Comm comm )
MPI_Comm /* comm */)
{
int i;
@ -105,7 +105,7 @@ void Compute_Bonded_ForcesOMP( reax_system *system, control_params *control,
void Compute_NonBonded_ForcesOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
MPI_Comm comm )
MPI_Comm /* comm */)
{
/* van der Waals and Coulomb interactions */
#ifdef OMP_TIMING
@ -133,7 +133,7 @@ void Compute_NonBonded_ForcesOMP( reax_system *system, control_params *control,
Saves enormous time & space! */
void Compute_Total_ForceOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, mpi_datatypes *mpi_data )
reax_list **lists, mpi_datatypes * /* mpi_data */)
{
#ifdef OMP_TIMING
double startTimeBase,endTimeBase;
@ -262,7 +262,7 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control,
/* ---------------------------------------------------------------------- */
void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lists,
void Validate_ListsOMP( reax_system *system, storage * /*workspace */, reax_list **lists,
int step, int n, int N, int numH, MPI_Comm comm )
{
int i, comp, Hindex;
@ -329,7 +329,7 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis
void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
reax_list **lists, output_controls * /* out_control */,
MPI_Comm comm ) {
#ifdef OMP_TIMING
double startTimeBase, endTimeBase;

2
src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
View File

@ -45,7 +45,7 @@ using namespace LAMMPS_NS;
void Hydrogen_BondsOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
reax_list **lists, output_controls * /* out_control */)
{
#ifdef OMP_TIMING
double endTimeBase, startTimeBase;

4
src/USER-OMP/reaxc_init_md_omp.cpp
View File

@ -48,8 +48,8 @@ extern int Init_Workspace(reax_system*, control_params*, storage*, MPI_Comm, cha
/* ---------------------------------------------------------------------- */
int Init_ListsOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
simulation_data * /* data */, storage * /* workspace */,
reax_list **lists, mpi_datatypes *mpi_data, char * /* msg */)
{
int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;

4
src/USER-OMP/reaxc_multi_body_omp.cpp
View File

@ -42,9 +42,9 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void Atom_EnergyOMP( reax_system *system, control_params *control,
void Atom_EnergyOMP( reax_system *system, control_params * /* control */,
simulation_data *data, storage *workspace, reax_list **lists,
output_controls *out_control )
output_controls * /* out_control */)
{
#ifdef OMP_TIMING
double endTimeBase, startTimeBase;

6
src/USER-OMP/reaxc_nonbonded_omp.cpp
View File

@ -47,8 +47,8 @@ using namespace LAMMPS_NS;
void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control ) {
reax_list **lists, output_controls * /* out_control */ )
{
int natoms = system->n;
reax_list *far_nbrs = (*lists) + FAR_NBRS;
double p_vdW1 = system->reax_param.gp.l[28];
@ -254,7 +254,7 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists,
output_controls *out_control ) {
output_controls * /* out_control */) {
double SMALL = 0.0001;
int natoms = system->n;

2
src/USER-OMP/reaxc_valence_angles_omp.cpp
View File

@ -100,7 +100,7 @@ void Calculate_dCos_ThetaOMP( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_
played by j which sits in the middle of the other two. */
void Valence_AnglesOMP( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
reax_list **lists, output_controls * /* out_control */)
{
#ifdef OMP_TIMING

2
src/USER-PTM/ptm_canonical_coloured.cpp
View File

@ -1,4 +1,4 @@
#include <string.h>
#include <cstring>
#include <climits>
#include <algorithm>
#include "ptm_graph_tools.h"

2
src/USER-PTM/ptm_convex_hull_incremental.cpp
View File

@ -1,6 +1,6 @@
#include <cmath>
#include <cfloat>
#include <string.h>
#include <cstring>
#include <cassert>
#include <algorithm>
#include "ptm_convex_hull_incremental.h"

2
src/USER-PTM/ptm_graph_tools.cpp
View File

@ -1,4 +1,4 @@
#include <string.h>
#include <cstring>
#include <algorithm>
#include "ptm_graph_tools.h"
#include "ptm_constants.h"

2
src/USER-PTM/ptm_index.cpp
View File

@ -1,6 +1,6 @@
#include <cstdio>
#include <cstdlib>
#include <string.h>
#include <cstring>
#include <cmath>
#include <cfloat>
#include <cassert>

2
src/USER-PTM/ptm_initialize_data.cpp
View File

@ -1,6 +1,6 @@
#include <cstdio>
#include <cstdlib>
#include <string.h>
#include <cstring>
#include <cmath>
#include <cfloat>
#include <cassert>

2
src/USER-PTM/ptm_polar.cpp
View File

@ -87,7 +87,7 @@
#include <cmath>
#include <algorithm>
#include <string.h>
#include <cstring>
#include "ptm_quat.h"
#include "ptm_polar.h"

2
src/USER-PTM/ptm_quat.cpp
View File

@ -1,4 +1,4 @@
#include <string.h>
#include <cstring>
#include <cmath>
#include <cfloat>

2
src/USER-PTM/ptm_structure_matcher.cpp
View File

@ -1,6 +1,6 @@
#include <cstdio>
#include <cstdlib>
#include <string.h>
#include <cstring>
#include <cmath>
#include <cfloat>
#include <cassert>

2
src/USER-REAXC/reaxc_io_tools.cpp
View File

@ -38,7 +38,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
output_controls *out_control, mpi_datatypes *mpi_data,
char *msg )
{
char temp[MAX_STR];
char temp[MAX_STR+8];
int ret;
if( out_control->write_steps > 0 ){

2
src/USER-REAXC/reaxc_tool_box.cpp
View File

@ -43,7 +43,7 @@ int Tokenize( char* s, char*** tok )
char *word;
int count=0;
strncpy( test, s, MAX_LINE );
strncpy( test, s, MAX_LINE-1);
for( word = strtok(test, sep); word; word = strtok(NULL, sep) ) {
strncpy( (*tok)[count], word, MAX_LINE );

2
src/USER-REAXC/reaxc_traj.cpp
View File

@ -315,7 +315,7 @@ int Init_Traj( reax_system *system, control_params *control,
output_controls *out_control, mpi_datatypes *mpi_data,
char *msg )
{
char fname[MAX_STR];
char fname[MAX_STR+8];
int atom_line_len[ NR_OPT_ATOM ] = { 0, 0, 0, 0,
ATOM_BASIC_LEN, ATOM_wV_LEN,
ATOM_wF_LEN, ATOM_FULL_LEN };

68
src/write_coeff.cpp
View File

@ -27,6 +27,8 @@
using namespace LAMMPS_NS;
enum {REGULAR_MODE, CLASS2_MODE};
/* ----------------------------------------------------------------------
called as write_coeff command in input script
------------------------------------------------------------------------- */
@ -50,6 +52,7 @@ void WriteCoeff::command(int narg, char **arg)
if (comm->me == 0) {
char str[256], coeff[256];
FILE *one = fopen(file,"wb+");
if (one == NULL) {
snprintf(str,256,"Cannot open coeff file %s",file);
error->one(FLERR,str);
@ -91,17 +94,78 @@ void WriteCoeff::command(int narg, char **arg)
}
fprintf(two,"# LAMMPS coeff file via write_coeff, version %s\n",
universe->version);
while(1) {
int coeff_mode = REGULAR_MODE;
if (fgets(str,256,one) == NULL) break;
// some coeffs need special treatment
if (strstr(str,"class2") != NULL) {
if (strstr(str,"angle_style") != NULL)
coeff_mode = CLASS2_MODE;
else if (strstr(str,"dihedral_style") != NULL)
coeff_mode = CLASS2_MODE;
else if (strstr(str,"improper_style") != NULL)
coeff_mode = CLASS2_MODE;
}
const char *section = (const char *)"";
fputs(str,two); // style
fgets(str,256,one); // coeff
n = strlen(str);
strcpy(coeff,str);
coeff[n-1] = '\0';
fgets(str,256,one);
while (strcmp(str,"end\n") != 0) {
fprintf(two,"%s %s",coeff,str);
fgets(str,256,one);
if (coeff_mode == REGULAR_MODE) {
fprintf(two,"%s %s",coeff,str);
fgets(str,256,one);
} else if (coeff_mode == CLASS2_MODE) {
// class2 angles, dihedrals, and impropers can have
// multiple sections and thus need special treatment
if (strcmp(str,"\n") == 0) {
// all but the the last section end with an empty line.
// skip it and read and parse the next section title
fgets(str,256,one);
if (strcmp(str,"BondBond Coeffs\n") == 0)
section = (const char *)"bb";
else if (strcmp(str,"BondAngle Coeffs\n") ==0)
section = (const char *)"ba";
else if (strcmp(str,"MiddleBondTorsion Coeffs\n") == 0)
section = (const char *)"mbt";
else if (strcmp(str,"EndBondTorsion Coeffs\n") == 0)
section = (const char *)"ebt";
else if (strcmp(str,"AngleTorsion Coeffs\n") == 0)
section = (const char *)"at";
else if (strcmp(str,"AngleAngleTorsion Coeffs\n") == 0)
section = (const char *)"aat";
else if (strcmp(str,"BondBond13 Coeffs\n") == 0)
section = (const char *)"bb13";
else if (strcmp(str,"AngleAngle Coeffs\n") == 0)
section = (const char *)"aa";
fgets(str,256,one); // gobble up one more empty line
fgets(str,256,one);
}
// parse type number and skip over it
int type = atoi(str);
char *p = str;
while ((*p != '\0') && (*p == ' ')) ++p;
while ((*p != '\0') && isdigit(*p)) ++p;
fprintf(two,"%s %d %s %s",coeff,type,section,p);
fgets(str,256,one);
}
}
fputc('\n',two);
}