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

lib/atc/LammpsInterface.h

@@ -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);
   /*@}*/
 

src/FLD/pair_lubricateU_poly.cpp

@@ -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]);
+  mu = force->numeric(FLERR,arg[0]);
-  flaglog = atoi(arg[1]);
+  flaglog = force->inumeric(FLERR,arg[1]);
-  cut_inner_global = atof(arg[2]);
+  cut_inner_global = force->numeric(FLERR,arg[2]);
-  cut_global = atof(arg[3]);
+  cut_global = force->numeric(FLERR,arg[3]);
-  gdot =  atof(arg[4]);
+  gdot =  force->numeric(FLERR,arg[4]);
 
   flagHI = flagVF = 1;
-  if (narg >= 6) flagHI = atoi(arg[5]);
+  if (narg >= 6) flagHI = force->inumeric(FLERR,arg[5]);
-  if (narg == 7) flagVF = atoi(arg[6]);
+  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; "

src/GPU/fix_gpu.cpp

@@ -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]);
+  first_gpu = force->inumeric(FLERR,arg[4]);
-  last_gpu = atoi(arg[5]);
+  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");
 

src/KSPACE/fix_tune_kspace.cpp

@@ -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
 

src/KSPACE/pppm_old.cpp

@@ -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];

src/MAKE/Makefile.mingw

@@ -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)

src/MANYBODY/pair_bop.cpp

@@ -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];
+          dPiB1=-.5*(cube(ABrtR1)+cube(ABrtR2))*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];
+          dPiB2=.25*BBrtR*(cube(ABrtR2)-cube(ABrtR1))*pi_c[iij]*pi_a[iij]*betaP[temp_ij];
-          dPiB3=((ABrtR1+ABrtR2)*pi_a[iij]-(pow(ABrtR1,3)+pow(ABrtR2,3))*pi_a[iij]
+          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;
+          dPiB1=-.5*(cube(ABrtR1)+cube(ABrtR2))*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;
+          dPiB2=.25*BBrtR*(cube(ABrtR2)-cube(ABrtR1))*pi_c[iij]*pi_a[iij]*betaP_ij;
-          dPiB3=((ABrtR1+ABrtR2)*pi_a[iij]-(pow(ABrtR1,3)+pow(ABrtR2,3))*pi_a[iij]
+          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));
         }
       }

src/MANYBODY/pair_tersoff_zbl.cpp

@@ -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
 

src/OPT/pair_lj_cut_tip4p_long_opt.cpp

@@ -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

src/REPLICA/neb.cpp

@@ -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]);
+  etol = force->numeric(FLERR,arg[0]);
-  ftol = atof(arg[1]);
+  ftol = force->numeric(FLERR,arg[1]);
-  n1steps = atoi(arg[2]);
+  n1steps = force->inumeric(FLERR,arg[2]);
-  n2steps = atoi(arg[3]);
+  n2steps = force->inumeric(FLERR,arg[3]);
-  nevery = atoi(arg[4]);
+  nevery = force->inumeric(FLERR,arg[4]);
   infile = arg[5];
 
   // error checks

src/REPLICA/prd.cpp

@@ -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]);
+  nsteps = force->inumeric(FLERR,arg[0]);
-  t_event = atoi(arg[1]);
+  t_event = force->inumeric(FLERR,arg[1]);
-  n_dephase = atoi(arg[2]);
+  n_dephase = force->inumeric(FLERR,arg[2]);
-  t_dephase = atoi(arg[3]);
+  t_dephase = force->inumeric(FLERR,arg[3]);
-  t_corr = atoi(arg[4]);
+  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]);
 

src/REPLICA/tad.cpp

@@ -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]);
+  nsteps = force->inumeric(FLERR,arg[0]);
-  t_event = atoi(arg[1]);
+  t_event = force->inumeric(FLERR,arg[1]);
-  templo = atof(arg[2]);
+  templo = force->numeric(FLERR,arg[2]);
-  temphi = atof(arg[3]);
+  temphi = force->numeric(FLERR,arg[3]);
-  delta_conf = atof(arg[4]);
+  delta_conf = force->numeric(FLERR,arg[4]);
-  tmax = atof(arg[5]);
+  tmax = force->numeric(FLERR,arg[5]);
 
   char *id_compute = new char[strlen(arg[6])+1];
   strcpy(id_compute,arg[6]);

src/REPLICA/temper.cpp

@@ -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]);
+  int nsteps = force->inumeric(FLERR,arg[0]);
-  nevery = atoi(arg[1]);
+  nevery = force->inumeric(FLERR,arg[1]);
-  double temp = atof(arg[2]);
+  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_swap = force->inumeric(FLERR,arg[4]);
-  seed_boltz = atoi(arg[5]);
+  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
 

src/RIGID/fix_rigid_nh.cpp

@@ -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;

src/XTC/xdr_compat.h

@@ -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

src/fix_adapt.cpp

@@ -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

src/min.cpp

@@ -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");

src/minimize.cpp

@@ -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->etol = force->numeric(FLERR,arg[0]);
-  update->ftol = atof(arg[1]);
+  update->ftol = force->numeric(FLERR,arg[1]);
-  update->nsteps = atoi(arg[2]);
+  update->nsteps = force->inumeric(FLERR,arg[2]);
-  update->max_eval = atoi(arg[3]);
+  update->max_eval = force->inumeric(FLERR,arg[3]);
 
   if (update->etol < 0.0 || update->ftol < 0.0)
     error->all(FLERR,"Illegal minimize command");

src/pair.cpp

@@ -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 itype = force->inumeric(FLERR,arg[0]);
-  int jtype = atoi(arg[1]);
+  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 inner = force->numeric(FLERR,arg[4]);
-  double outer = atof(arg[5]);
+  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[0] = force->numeric(FLERR,arg[8]);
-    q[1] = atof(arg[9]);
+    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;
 }
+

src/rerun.cpp

@@ -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) {

src/respa.cpp

@@ -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;
+      level_inner = force->inumeric(FLERR,arg[iarg+1]) - 1;
-      cutoff[0] = atof(arg[iarg+2]);
+      cutoff[0] = force->numeric(FLERR,arg[iarg+2]);
-      cutoff[1] = atof(arg[iarg+3]);
+      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;
+      level_middle = force->inumeric(FLERR,arg[iarg+1]) - 1;
-      cutoff[2] = atof(arg[iarg+2]);
+      cutoff[2] = force->numeric(FLERR,arg[iarg+2]);
-      cutoff[3] = atof(arg[iarg+3]);
+      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");
   }

src/run.cpp

@@ -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;

src/universe.cpp

@@ -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)