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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10199 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-06-29 21:27:42 +00:00
parent e954b14d99
commit b0007d45b7
23 changed files with 109 additions and 209 deletions
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2
lib/atc/LammpsInterface.h
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@ -259,7 +259,7 @@ class LammpsInterface {
/*@{*/
int atomPE_create(void);
void atomPE_init(void);
void atomPE_addstep(int step);
void atomPE_addstep(LAMMPS_NS::bigint step);
double * atomPE_compute(void);
/*@}*/

14
src/FLD/pair_lubricateU_poly.cpp
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@ -1127,15 +1127,15 @@ void PairLubricateUPoly::settings(int narg, char **arg)
if (narg < 5 || narg > 7) error->all(FLERR,"Illegal pair_style command");
mu = atof(arg[0]);
flaglog = atoi(arg[1]);
cut_inner_global = atof(arg[2]);
cut_global = atof(arg[3]);
gdot = atof(arg[4]);
mu = force->numeric(FLERR,arg[0]);
flaglog = force->inumeric(FLERR,arg[1]);
cut_inner_global = force->numeric(FLERR,arg[2]);
cut_global = force->numeric(FLERR,arg[3]);
gdot = force->numeric(FLERR,arg[4]);
flagHI = flagVF = 1;
if (narg >= 6) flagHI = atoi(arg[5]);
if (narg == 7) flagVF = atoi(arg[6]);
if (narg >= 6) flagHI = force->inumeric(FLERR,arg[5]);
if (narg == 7) flagVF = force->inumeric(FLERR,arg[6]);
if (flaglog == 1 && flagHI == 0) {
error->warning(FLERR,"Cannot include log terms without 1/r terms; "

10
src/GPU/fix_gpu.cpp
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@ -68,8 +68,8 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
} else
error->all(FLERR,"Illegal fix GPU command");
first_gpu = atoi(arg[4]);
last_gpu = atoi(arg[5]);
first_gpu = force->inumeric(FLERR,arg[4]);
last_gpu = force->inumeric(FLERR,arg[5]);
_particle_split = force->numeric(FLERR,arg[6]);
if (_particle_split==0 || _particle_split>1)
@ -84,11 +84,11 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
if (iarg+2 > narg) error->all(FLERR,"Illegal fix GPU command");
if (strcmp(arg[iarg],"threads_per_atom") == 0)
threads_per_atom = atoi(arg[iarg+1]);
threads_per_atom = force->inumeric(FLERR,arg[iarg+1]);
else if (strcmp(arg[iarg],"nthreads") == 0)
nthreads = atoi(arg[iarg+1]);
nthreads = force->inumeric(FLERR,arg[iarg+1]);
else if (strcmp(arg[iarg],"cellsize") == 0)
cell_size = atof(arg[iarg+1]);
cell_size = force->numeric(FLERR,arg[iarg+1]);
else
error->all(FLERR,"Illegal fix GPU command");

2
src/KSPACE/fix_tune_kspace.cpp
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@ -63,7 +63,7 @@ FixTuneKspace::FixTuneKspace(LAMMPS *lmp, int narg, char **arg) :
// parse arguments
nevery = atoi(arg[3]);
nevery = force->inumeric(FLERR,arg[3]);
// set up reneighboring

2
src/KSPACE/pppm_old.cpp
View File

@ -64,7 +64,7 @@ PPPMOld::PPPMOld(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
pppmflag = 1;
group_group_enable = 1;
accuracy_relative = atof(arg[0]);
accuracy_relative = fabs(force->numeric(FLERR,arg[0]));
nfactors = 3;
factors = new int[nfactors];

113
src/MAKE/Makefile.mingw
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@ -1,113 +0,0 @@
# mingw = Windows 32bit, cross-compiled on Linux, gcc-4.4.1, MinGW x-compiler
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = i686-pc-mingw32-g++
CCFLAGS = -O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
-fno-exceptions -fno-rtti -ffast-math -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = i686-pc-mingw32-g++
LINKFLAGS = -O
LIB = -lwsock32 # -lwsock32 is needed for USER-IMD which uses tcp/ip sockets.
SIZE = i686-pc-mingw32-size
ARCHIVE = ar
ARFLAGS = -rcsv
SHLIBFLAGS = -shared
# ---------------------------------------------------------------------
# LAMMPS-specific settings
# specify settings for LAMMPS features you will use
# if you change any -D setting, do full re-compile after "make clean"
# LAMMPS ifdef settings, OPTIONAL
# see possible settings in doc/Section_start.html#2_2 (step 4)
LMP_INC = -DLAMMPS_XDR # -DLAMMPS_GZIP -DMALLOC_MEMALIGN=64
# MPI library, REQUIRED
# see discussion in doc/Section_start.html#2_2 (step 5)
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library
MPI_INC = -I../STUBS
MPI_PATH =
MPI_LIB = mpi.o
# FFT library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 6)
# can be left blank to use provided KISS FFT library
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
# PATH = path for FFT library
# LIB = name of FFT library
FFT_INC = -DFFT_NONE #-DFFT_SINGLE
FFT_PATH =
FFT_LIB = #-lfftw
# JPEG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# only needed if -DLAMMPS_JPEG listed with LMP_INC
# INC = path for jpeglib.h
# PATH = path for JPEG library
# LIB = name of JPEG library
JPG_INC =
JPG_PATH =
JPG_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# no need to edit this section
include Makefile.package.settings
include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
# Path to src files
vpath %.cpp ..
vpath %.h ..
# Link target
$(EXE): $(EXE).exe ../MAKE/mingw_cross.nsis
makensis ../MAKE/mingw_cross.nsis
(cd ..; zip -0 lammps-icms-win.zip lammps-icms-win.exe)
touch $(EXE)
$(EXE).exe: $(OBJ) mpi.o
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE).exe
$(SIZE) $(EXE).exe
# Library target
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
# Compilation rules
%.o:%.cpp
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
%.d:%.cpp
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
# Individual dependencies
mpi.o: ../STUBS/mpi.c ../STUBS/mpi.h
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
DEPENDS = $(OBJ:.o=.d)
sinclude $(DEPENDS)

16
src/MANYBODY/pair_bop.cpp
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@ -50,8 +50,10 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "math_special.h"
using namespace LAMMPS_NS;
using namespace MathSpecial;
#define MAXLINE 1024
#define EPSILON 1.0e-6
@ -7223,9 +7225,9 @@ void PairBOP::PiBo()
// piB is similary formulation to (a) Eq. 36 and (b) Eq. 18
piB[n]=(ABrtR1+ABrtR2)*pi_a[iij]*betaP[temp_ij];
dPiB1=-.5*(pow(ABrtR1,3)+pow(ABrtR2,3))*pi_c[iij]*pi_a[iij]*betaP[temp_ij];
dPiB2=.25*BBrtR*(pow(ABrtR2,3)-pow(ABrtR1,3))*pi_c[iij]*pi_a[iij]*betaP[temp_ij];
dPiB3=((ABrtR1+ABrtR2)*pi_a[iij]-(pow(ABrtR1,3)+pow(ABrtR2,3))*pi_a[iij]
dPiB1=-.5*(cube(ABrtR1)+cube(ABrtR2))*pi_c[iij]*pi_a[iij]*betaP[temp_ij];
dPiB2=.25*BBrtR*(cube(ABrtR2)-cube(ABrtR1))*pi_c[iij]*pi_a[iij]*betaP[temp_ij];
dPiB3=((ABrtR1+ABrtR2)*pi_a[iij]-(cube(ABrtR1)+cube(ABrtR2))*pi_a[iij]
*betaP[temp_ij]*betaP[temp_ij])*dBetaP[temp_ij]/rij[temp_ij];
n++;
pp2=2.0*betaP[temp_ij];
@ -8147,9 +8149,9 @@ void PairBOP::PiBo_otf()
// piB is similary formulation to (a) Eq. 36 and (b) Eq. 18
piB[n]=(ABrtR1+ABrtR2)*pi_a[iij]*betaP_ij;
dPiB1=-.5*(pow(ABrtR1,3)+pow(ABrtR2,3))*pi_c[iij]*pi_a[iij]*betaP_ij;
dPiB2=.25*BBrtR*(pow(ABrtR2,3)-pow(ABrtR1,3))*pi_c[iij]*pi_a[iij]*betaP_ij;
dPiB3=((ABrtR1+ABrtR2)*pi_a[iij]-(pow(ABrtR1,3)+pow(ABrtR2,3))*pi_a[iij]
dPiB1=-.5*(cube(ABrtR1)+cube(ABrtR2))*pi_c[iij]*pi_a[iij]*betaP_ij;
dPiB2=.25*BBrtR*(cube(ABrtR2)-cube(ABrtR1))*pi_c[iij]*pi_a[iij]*betaP_ij;
dPiB3=((ABrtR1+ABrtR2)*pi_a[iij]-(cube(ABrtR1)+cube(ABrtR2))*pi_a[iij]
*betaP_ij*betaP_ij)*dBetaP_ij/r_ij;
n++;
@ -9017,7 +9019,7 @@ void PairBOP::setSign()
cs=0.0;
if(xBO<alpha)
cs=32.0*(alpha-xBO);
bigF=(sigma_f[i]*(1.0-sigma_f[i])-fth*(1.0-fth))/pow(1.0-2.0*fth,2);
bigF=(sigma_f[i]*(1.0-sigma_f[i])-fth*(1.0-fth))/square(1.0-2.0*fth);
FsigBO[i][j]=2.0*fth+2.0*bigF*(1.0-2.0*fth)*(1.0+bigF*(1.0-cs*bigF));
}
}

2
src/MANYBODY/pair_tersoff_zbl.cpp
View File

@ -68,7 +68,7 @@ void PairTersoffZBL::read_file(char *file)
memory->sfree(params);
params = NULL;
nparams = 0;
nparams = maxparam = 0;
// open file on proc 0

21
src/OPT/pair_lj_cut_tip4p_long_opt.cpp
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@ -106,19 +106,19 @@ template < const int CTABLE, const int EVFLAG,
const int EFLAG, const int VFLAG>
void PairLJCutTIP4PLongOpt::eval()
{
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double fraction,table;
double r,rsq,r2inv,r6inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double v[6],xH1[3],xH2[3];
double fdx,fdy,fdz,fOx,fOy,fOz,fHx,fHy,fHz;
const double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
int i,j,ii,jj,inum,jnum,itype,jtype,itable,key;
int n,vlist[6];
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double fraction,table;
double delxOM,delyOM,delzOM;
double r,rsq,r2inv,r6inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc,ddotf;
double v[6],xH1[3],xH2[3];
double fdx,fdy,fdz,f1x,f1y,f1z,fOx,fOy,fOz,fHx,fHy,fHz;
const double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
@ -434,7 +434,6 @@ void PairLJCutTIP4PLongOpt::eval()
}
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
compute position xM of fictitious charge site for O atom and 2 H atoms
return it as xM

11
src/REPLICA/neb.cpp
View File

@ -31,6 +31,7 @@
#include "timer.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
@ -105,11 +106,11 @@ void NEB::command(int narg, char **arg)
if (narg != 6) error->universe_all(FLERR,"Illegal NEB command");
etol = atof(arg[0]);
ftol = atof(arg[1]);
n1steps = atoi(arg[2]);
n2steps = atoi(arg[3]);
nevery = atoi(arg[4]);
etol = force->numeric(FLERR,arg[0]);
ftol = force->numeric(FLERR,arg[1]);
n1steps = force->inumeric(FLERR,arg[2]);
n2steps = force->inumeric(FLERR,arg[3]);
nevery = force->inumeric(FLERR,arg[4]);
infile = arg[5];
// error checks

12
src/REPLICA/prd.cpp
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@ -73,15 +73,15 @@ void PRD::command(int narg, char **arg)
if (narg < 7) error->universe_all(FLERR,"Illegal prd command");
nsteps = atoi(arg[0]);
t_event = atoi(arg[1]);
n_dephase = atoi(arg[2]);
t_dephase = atoi(arg[3]);
t_corr = atoi(arg[4]);
nsteps = force->inumeric(FLERR,arg[0]);
t_event = force->inumeric(FLERR,arg[1]);
n_dephase = force->inumeric(FLERR,arg[2]);
t_dephase = force->inumeric(FLERR,arg[3]);
t_corr = force->inumeric(FLERR,arg[4]);
char *id_compute = new char[strlen(arg[5])+1];
strcpy(id_compute,arg[5]);
int seed = atoi(arg[6]);
int seed = force->inumeric(FLERR,arg[6]);
options(narg-7,&arg[7]);

12
src/REPLICA/tad.cpp
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@ -91,12 +91,12 @@ void TAD::command(int narg, char **arg)
if (narg < 7) error->universe_all(FLERR,"Illegal tad command");
nsteps = atoi(arg[0]);
t_event = atoi(arg[1]);
templo = atof(arg[2]);
temphi = atof(arg[3]);
delta_conf = atof(arg[4]);
tmax = atof(arg[5]);
nsteps = force->inumeric(FLERR,arg[0]);
t_event = force->inumeric(FLERR,arg[1]);
templo = force->numeric(FLERR,arg[2]);
temphi = force->numeric(FLERR,arg[3]);
delta_conf = force->numeric(FLERR,arg[4]);
tmax = force->numeric(FLERR,arg[5]);
char *id_compute = new char[strlen(arg[6])+1];
strcpy(id_compute,arg[6]);

12
src/REPLICA/temper.cpp
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@ -70,20 +70,20 @@ void Temper::command(int narg, char **arg)
if (narg != 6 && narg != 7)
error->universe_all(FLERR,"Illegal temper command");
int nsteps = atoi(arg[0]);
nevery = atoi(arg[1]);
double temp = atof(arg[2]);
int nsteps = force->inumeric(FLERR,arg[0]);
nevery = force->inumeric(FLERR,arg[1]);
double temp = force->numeric(FLERR,arg[2]);
for (whichfix = 0; whichfix < modify->nfix; whichfix++)
if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
if (whichfix == modify->nfix)
error->universe_all(FLERR,"Tempering fix ID is not defined");
seed_swap = atoi(arg[4]);
seed_boltz = atoi(arg[5]);
seed_swap = force->inumeric(FLERR,arg[4]);
seed_boltz = force->inumeric(FLERR,arg[5]);
my_set_temp = universe->iworld;
if (narg == 7) my_set_temp = atoi(arg[6]);
if (narg == 7) my_set_temp = force->inumeric(FLERR,arg[6]);
// swap frequency must evenly divide total # of timesteps

2
src/RIGID/fix_rigid_nh.cpp
View File

@ -612,7 +612,7 @@ void FixRigidNH::final_integrate()
// sum over atoms to get force and torque on rigid body
int *image = atom->image;
tagint *image = atom->image;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;

2
src/XTC/xdr_compat.h
View File

@ -60,7 +60,7 @@ extern "C" {
typedef int bool_t;
#if defined(__MINGW32_VERSION)
#if defined(__MINGW32__)
typedef char * caddr_t;
typedef unsigned int u_int;
#endif

2
src/fix_adapt.cpp
View File

@ -40,7 +40,7 @@ enum{DIAMETER,CHARGE};
FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal fix adapt command");
nevery = atoi(arg[3]);
nevery = force->inumeric(FLERR,arg[3]);
if (nevery < 0) error->all(FLERR,"Illegal fix adapt command");
// count # of adaptations

2
src/min.cpp
View File

@ -606,7 +606,7 @@ void Min::modify_params(int narg, char **arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"dmax") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");
dmax = atof(arg[iarg+1]);
dmax = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"line") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command");

9
src/minimize.cpp
View File

@ -19,6 +19,7 @@
#include "finish.h"
#include "timer.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
@ -35,10 +36,10 @@ void Minimize::command(int narg, char **arg)
if (domain->box_exist == 0)
error->all(FLERR,"Minimize command before simulation box is defined");
update->etol = atof(arg[0]);
update->ftol = atof(arg[1]);
update->nsteps = atoi(arg[2]);
update->max_eval = atoi(arg[3]);
update->etol = force->numeric(FLERR,arg[0]);
update->ftol = force->numeric(FLERR,arg[1]);
update->nsteps = force->inumeric(FLERR,arg[2]);
update->max_eval = force->inumeric(FLERR,arg[3]);
if (update->etol < 0.0 || update->ftol < 0.0)
error->all(FLERR,"Illegal minimize command");

31
src/pair.cpp
View File

@ -127,23 +127,23 @@ void Pair::modify_params(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"table") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
ncoultablebits = atoi(arg[iarg+1]);
ncoultablebits = force->inumeric(FLERR,arg[iarg+1]);
if (ncoultablebits > sizeof(float)*CHAR_BIT)
error->all(FLERR,"Too many total bits for bitmapped lookup table");
iarg += 2;
} else if (strcmp(arg[iarg],"table/disp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
ndisptablebits = atoi(arg[iarg+1]);
ndisptablebits = force->inumeric(FLERR,arg[iarg+1]);
if (ndisptablebits > sizeof(float)*CHAR_BIT)
error->all(FLERR,"Too many total bits for bitmapped lookup table");
iarg += 2;
} else if (strcmp(arg[iarg],"tabinner") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
tabinner = atof(arg[iarg+1]);
tabinner = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"tabinner/disp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
tabinner_disp = atof(arg[iarg+1]);
tabinner_disp = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"tail") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
@ -1449,12 +1449,12 @@ void Pair::write_file(int narg, char **arg)
// parse arguments
int itype = atoi(arg[0]);
int jtype = atoi(arg[1]);
int itype = force->inumeric(FLERR,arg[0]);
int jtype = force->inumeric(FLERR,arg[1]);
if (itype < 1 || itype > atom->ntypes || jtype < 1 || jtype > atom->ntypes)
error->all(FLERR,"Invalid atom types in pair_write command");
int n = atoi(arg[2]);
int n = force->inumeric(FLERR,arg[2]);
int style;
if (strcmp(arg[3],"r") == 0) style = RLINEAR;
@ -1462,8 +1462,8 @@ void Pair::write_file(int narg, char **arg)
else if (strcmp(arg[3],"bitmap") == 0) style = BMP;
else error->all(FLERR,"Invalid style in pair_write command");
double inner = atof(arg[4]);
double outer = atof(arg[5]);
double inner = force->numeric(FLERR,arg[4]);
double outer = force->numeric(FLERR,arg[5]);
if (inner <= 0.0 || inner >= outer)
error->all(FLERR,"Invalid cutoffs in pair_write command");
@ -1503,8 +1503,8 @@ void Pair::write_file(int narg, char **arg)
double q[2];
q[0] = q[1] = 1.0;
if (narg == 10) {
q[0] = atof(arg[8]);
q[1] = atof(arg[9]);
q[0] = force->numeric(FLERR,arg[8]);
q[1] = force->numeric(FLERR,arg[9]);
}
double *q_hold;
@ -1623,6 +1623,8 @@ FILE *Pair::open_potential(const char *name)
{
FILE *fp;
if (name == NULL) return NULL;
// attempt to open file directly
// if successful, return ptr
@ -1635,10 +1637,12 @@ FILE *Pair::open_potential(const char *name)
if (path == NULL) return NULL;
const char *pot = potname(name);
if (pot == NULL) return NULL;
size_t len1 = strlen(path);
size_t len2 = strlen(pot);
char *newpath = new char[len1+len2+2];
char *newpath = new char[len1+len2];
strcpy(newpath,path);
#if defined(_WIN32)
newpath[len1] = '\\';
@ -1662,6 +1666,8 @@ const char *Pair::potname(const char *path)
{
const char *pot;
if (path == NULL) return NULL;
#if defined(_WIN32)
// skip over the disk drive part of windows pathnames
if (isalpha(path[0]) && path[1] == ':')
@ -1687,3 +1693,4 @@ double Pair::memory_usage()
bytes += comm->nthreads*maxvatom*6 * sizeof(double);
return bytes;
}

5
src/rerun.cpp
View File

@ -24,6 +24,7 @@
#include "finish.h"
#include "timer.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
@ -80,12 +81,12 @@ void Rerun::command(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
nevery = atoi(arg[iarg+1]);
nevery = force->inumeric(FLERR,arg[iarg+1]);
if (nevery < 0) error->all(FLERR,"Illegal rerun command");
iarg += 2;
} else if (strcmp(arg[iarg],"skip") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
nskip = atoi(arg[iarg+1]);
nskip = force->inumeric(FLERR,arg[iarg+1]);
if (nskip <= 0) error->all(FLERR,"Illegal rerun command");
iarg += 2;
} else if (strcmp(arg[iarg],"start") == 0) {

30
src/respa.cpp
View File

@ -46,13 +46,13 @@ Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg)
{
if (narg < 1) error->all(FLERR,"Illegal run_style respa command");
nlevels = atoi(arg[0]);
nlevels = force->inumeric(FLERR,arg[0]);
if (nlevels < 1) error->all(FLERR,"Respa levels must be >= 1");
if (narg < nlevels) error->all(FLERR,"Illegal run_style respa command");
loop = new int[nlevels];
for (int iarg = 1; iarg < nlevels; iarg++) {
loop[iarg-1] = atoi(arg[iarg]);
loop[iarg-1] = force->inumeric(FLERR,arg[iarg]);
if (loop[iarg-1] <= 0) error->all(FLERR,"Illegal run_style respa command");
}
loop[nlevels-1] = 1;
@ -68,43 +68,43 @@ Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command");
level_bond = atoi(arg[iarg+1]) - 1;
level_bond = force->inumeric(FLERR,arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command");
level_angle = atoi(arg[iarg+1]) - 1;
level_angle = force->inumeric(FLERR,arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command");
level_dihedral = atoi(arg[iarg+1]) - 1;
level_dihedral = force->inumeric(FLERR,arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"improper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command");
level_improper = atoi(arg[iarg+1]) - 1;
level_improper = force->inumeric(FLERR,arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command");
level_pair = atoi(arg[iarg+1]) - 1;
level_pair = force->inumeric(FLERR,arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"inner") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal run_style respa command");
level_inner = atoi(arg[iarg+1]) - 1;
cutoff[0] = atof(arg[iarg+2]);
cutoff[1] = atof(arg[iarg+3]);
level_inner = force->inumeric(FLERR,arg[iarg+1]) - 1;
cutoff[0] = force->numeric(FLERR,arg[iarg+2]);
cutoff[1] = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"middle") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal run_style respa command");
level_middle = atoi(arg[iarg+1]) - 1;
cutoff[2] = atof(arg[iarg+2]);
cutoff[3] = atof(arg[iarg+3]);
level_middle = force->inumeric(FLERR,arg[iarg+1]) - 1;
cutoff[2] = force->numeric(FLERR,arg[iarg+2]);
cutoff[3] = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"outer") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command");
level_outer = atoi(arg[iarg+1]) - 1;
level_outer = force->inumeric(FLERR,arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command");
level_kspace = atoi(arg[iarg+1]) - 1;
level_kspace = force->inumeric(FLERR,arg[iarg+1]) - 1;
iarg += 2;
} else error->all(FLERR,"Illegal run_style respa command");
}

3
src/run.cpp
View File

@ -23,6 +23,7 @@
#include "input.h"
#include "timer.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
@ -90,7 +91,7 @@ void Run::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal run command");
nevery = atoi(arg[iarg+1]);
nevery = force->inumeric(FLERR,arg[iarg+1]);
if (nevery <= 0) error->all(FLERR,"Illegal run command");
first = iarg+2;
last = narg-1;

3
src/universe.cpp
View File

@ -18,6 +18,7 @@
#include "universe.h"
#include "version.h"
#include "error.h"
#include "force.h"
#include "memory.h"
using namespace LAMMPS_NS;
@ -77,7 +78,7 @@ void Universe::reorder(char *style, char *arg)
if (uworld != uorig) MPI_Comm_free(&uworld);
if (strcmp(style,"nth") == 0) {
int n = atoi(arg);
int n = force->inumeric(FLERR,arg);
if (n <= 0)
error->universe_all(FLERR,"Invalid -reorder N value");
if (nprocs % n)