diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index baaf2f7b05..7ea3c2aafe 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -75,11 +75,10 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : // expand args if any have wildcard character "*" int expand = 0; - char **earg,**arghold; + char **earg; int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg); if (earg != &arg[iarg]) expand = 1; - arghold = arg; arg = earg; // parse values until one isn't recognized @@ -190,9 +189,8 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : // if wildcard expansion occurred, free earg memory from expand_args() if (expand) { - for (int i = 0; i < nvalues; i++) delete [] earg[i]; + for (int i = 0; i < nargnew; i++) delete [] earg[i]; memory->sfree(earg); - arg = arghold; } // setup and error check diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index e99533eba8..033614789a 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -68,13 +68,15 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) : // nfield may be shrunk below if extra optional args exist expand = 0; - nfield = input->expand_args(narg-5,&arg[5],1,earg); + nfield = nargnew = input->expand_args(narg-5,&arg[5],1,earg); if (earg != &arg[5]) expand = 1; // allocate field vectors pack_choice = new FnPtrPack[nfield]; vtype = new int[nfield]; + field2index = new int[nfield]; + argindex = new int[nfield]; buffer_allow = 1; buffer_flag = 1; @@ -87,9 +89,6 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) : // computes, fixes, variables which the dump accesses - memory->create(field2index,nfield,"dump:field2index"); - memory->create(argindex,nfield,"dump:argindex"); - ncompute = 0; id_compute = NULL; compute = NULL; @@ -181,14 +180,14 @@ DumpCustom::~DumpCustom() // could not do in constructor, b/c some derived classes process earg if (expand) { - for (int i = 0; i < nfield; i++) delete [] earg[i]; + for (int i = 0; i < nargnew; i++) delete [] earg[i]; memory->sfree(earg); } delete [] pack_choice; delete [] vtype; - memory->destroy(field2index); - memory->destroy(argindex); + delete [] field2index; + delete [] argindex; delete [] idregion; memory->destroy(thresh_array); diff --git a/src/dump_custom.h b/src/dump_custom.h index 3239a3283f..6caa70d1f7 100644 --- a/src/dump_custom.h +++ b/src/dump_custom.h @@ -40,6 +40,7 @@ class DumpCustom : public Dump { int expand; // flag for whether field args were expanded char **earg; // field names with wildcard expansion + int nargnew; // size of earg int *vtype; // type of each vector (INT, DOUBLE) char **vformat; // format string for each vector element diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index 9b0375baec..2784537c67 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -49,11 +49,10 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) : // this can reset nvalues int expand = 0; - char **earg,**arghold; + char **earg; nvalues = input->expand_args(nvalues,&arg[6],1,earg); if (earg != &arg[6]) expand = 1; - arghold = arg; arg = earg; // parse values @@ -128,7 +127,6 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) : if (expand) { for (int i = 0; i < nvalues; i++) delete [] earg[i]; memory->sfree(earg); - arg = arghold; } // setup and error check diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index ce3ccde1c6..dd3d69fac3 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -60,11 +60,10 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : // expand args if any have wildcard character "*" int expand = 0; - char **earg,**arghold; + char **earg; int nargnew = input->expand_args(narg-7,&arg[7],1,earg); if (earg != &arg[7]) expand = 1; - arghold = arg; arg = earg; // parse values until one isn't recognized @@ -377,9 +376,8 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : // wait to do this until after file comment lines are printed if (expand) { - for (int i = 0; i < nvalues; i++) delete [] earg[i]; + for (int i = 0; i < nargnew; i++) delete [] earg[i]; memory->sfree(earg); - arg = arghold; } // this fix produces a global array diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 0e2ad9d0f5..18e16d1ea9 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -59,11 +59,10 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): // expand args if any have wildcard character "*" int expand = 0; - char **earg,**arghold; + char **earg; int nargnew = input->expand_args(narg-6,&arg[6],0,earg); if (earg != &arg[6]) expand = 1; - arghold = arg; arg = earg; // parse values until one isn't recognized @@ -292,9 +291,8 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg): // wait to do this until after file comment lines are printed if (expand) { - for (int i = 0; i < nvalues; i++) delete [] earg[i]; + for (int i = 0; i < nargnew; i++) delete [] earg[i]; memory->sfree(earg); - arg = arghold; } // allocate and initialize memory for averaging diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index cc0eb9532e..06281e2eca 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -100,67 +100,58 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : // this can reset nvalues int expand = 0; - char **earg,**arghold; + char **earg; nvalues = input->expand_args(nvalues,&arg[9],mode,earg); if (earg != &arg[9]) expand = 1; - arghold = arg; arg = earg; // parse values - which = argindex = value2index = NULL; - ids = NULL; - allocate_values(nvalues); + which = new int[nvalues]; + argindex = new int[nvalues]; + value2index = new int[nvalues]; + ids = new char*[nvalues]; for (int i = 0; i < nvalues; i++) { if (strcmp(arg[i],"x") == 0) { which[i] = X; argindex[i] = 0; ids[i] = NULL; - iarg++; } else if (strcmp(arg[i],"y") == 0) { which[i] = X; argindex[i] = 1; ids[i] = NULL; - iarg++; } else if (strcmp(arg[i],"z") == 0) { which[i] = X; argindex[i] = 2; ids[i] = NULL; - iarg++; } else if (strcmp(arg[i],"vx") == 0) { which[i] = V; argindex[i] = 0; ids[i] = NULL; - iarg++; } else if (strcmp(arg[i],"vy") == 0) { which[i] = V; argindex[i] = 1; ids[i] = NULL; - iarg++; } else if (strcmp(arg[i],"vz") == 0) { which[i] = V; argindex[i] = 2; ids[i] = NULL; - iarg++; } else if (strcmp(arg[i],"fx") == 0) { which[i] = F; argindex[i] = 0; ids[i] = NULL; - iarg++; } else if (strcmp(arg[i],"fy") == 0) { which[i] = F; argindex[i] = 1; ids[i] = NULL; - iarg++; } else if (strcmp(arg[i],"fz") == 0) { which[i] = F; argindex[i] = 2; ids[i] = NULL; - iarg++; } else if ((strncmp(arg[i],"c_",2) == 0) || (strncmp(arg[i],"f_",2) == 0) || @@ -193,7 +184,6 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : if (expand) { for (int i = 0; i < nvalues; i++) delete [] earg[i]; memory->sfree(earg); - arg = arghold; } // setup and error check @@ -496,11 +486,11 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : FixAveHisto::~FixAveHisto() { - memory->destroy(which); - memory->destroy(argindex); - memory->destroy(value2index); + delete [] which; + delete [] argindex; + delete [] value2index; for (int i = 0; i < nvalues; i++) delete [] ids[i]; - memory->sfree(ids); + delete [] ids; if (fp && me == 0) fclose(fp); @@ -1003,18 +993,6 @@ void FixAveHisto::options(int iarg, int narg, char **arg) } } -/* ---------------------------------------------------------------------- - reallocate vectors for each input value, of length N -------------------------------------------------------------------------- */ - -void FixAveHisto::allocate_values(int n) -{ - memory->grow(which,n,"ave/hsito:which"); - memory->grow(argindex,n,"ave/histo:argindex"); - memory->grow(value2index,n,"ave/histo:value2index"); - ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/histo:ids"); -} - /* ---------------------------------------------------------------------- calculate nvalid = next step on which end_of_step does something can be this timestep if multiple of nfreq and nrepeat = 1 diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h index 6fcfd27e31..c740a26256 100644 --- a/src/fix_ave_histo.h +++ b/src/fix_ave_histo.h @@ -66,7 +66,6 @@ class FixAveHisto : public Fix { void bin_vector(int, double *, int); void bin_atoms(double *, int); void options(int, int, char **); - void allocate_values(int); bigint nextvalid(); }; diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index bbcef78f92..430c6069b7 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -79,18 +79,20 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) : // this can reset nvalues int expand = 0; - char **earg,**arghold; + char **earg; nvalues = input->expand_args(nvalues,&arg[6],mode,earg); if (earg != &arg[6]) expand = 1; - arghold = arg; arg = earg; // parse values - which = argindex = value2index = offcol = varlen = NULL; - ids = NULL; - allocate_values(nvalues); + which = new int[nvalues]; + argindex = new int[nvalues]; + value2index = new int[nvalues]; + offcol = new int[nvalues]; + varlen = new int[nvalues]; + ids = new char*[nvalues]; for (int i = 0; i < nvalues; i++) { if (arg[i][0] == 'c') which[i] = COMPUTE; @@ -293,7 +295,6 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) : if (expand) { for (int i = 0; i < nvalues; i++) delete [] earg[i]; memory->sfree(earg); - arg = arghold; } // allocate memory for averaging @@ -455,13 +456,13 @@ FixAveTime::~FixAveTime() delete [] format_user; - memory->destroy(which); - memory->destroy(argindex); - memory->destroy(value2index); - memory->destroy(offcol); - memory->destroy(varlen); + delete [] which; + delete [] argindex; + delete [] value2index; + delete [] offcol; + delete [] varlen; for (int i = 0; i < nvalues; i++) delete [] ids[i]; - memory->sfree(ids); + delete [] ids; delete [] extlist; @@ -1105,20 +1106,6 @@ void FixAveTime::options(int iarg, int narg, char **arg) } } -/* ---------------------------------------------------------------------- - reallocate vectors for N input values -------------------------------------------------------------------------- */ - -void FixAveTime::allocate_values(int n) -{ - memory->grow(which,n,"ave/time:which"); - memory->grow(argindex,n,"ave/time:argindex"); - memory->grow(value2index,n,"ave/time:value2index"); - memory->grow(offcol,n,"ave/time:offcol"); - memory->grow(varlen,n,"ave/time:varlen"); - ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/time:ids"); -} - /* ---------------------------------------------------------------------- reallocate arrays for mode = VECTOR of size Nrows x Nvalues ------------------------------------------------------------------------- */ diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h index f2f79f1276..d771036530 100644 --- a/src/fix_ave_time.h +++ b/src/fix_ave_time.h @@ -70,7 +70,6 @@ class FixAveTime : public Fix { void invoke_scalar(bigint); void invoke_vector(bigint); void options(int, int, char **); - void allocate_values(int); void allocate_arrays(); bigint nextvalid(); }; diff --git a/src/thermo.cpp b/src/thermo.cpp index 5474401b07..3ef19c50a6 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -569,7 +569,7 @@ void Thermo::modify_params(int narg, char **arg) format_int_user = NULL; format_bigint_user = NULL; format_float_user = NULL; - for (int i = 0; i < nfield_initial; i++) { + for (int i = 0; i < nfield_initial+1; i++) { delete [] format_column_user[i]; format_column_user[i] = NULL; } @@ -610,7 +610,7 @@ void Thermo::modify_params(int narg, char **arg) strcpy(format_float_user,arg[iarg+2]); } else { int i = force->inumeric(FLERR,arg[iarg+1]) - 1; - if (i < 0 || i >= nfield_initial) + if (i < 0 || i >= nfield_initial+1) error->all(FLERR,"Illegal thermo_modify command"); if (format_column_user[i]) delete [] format_column_user[i]; int n = strlen(arg[iarg+2]) + 1;