diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index c614577933..02cce5a014 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -115,25 +115,25 @@ FixOrientBCC::FixOrientBCC(LAMMPS *lmp, int narg, char **arg) : char *result; int count; - FILE *infile = fopen(xifilename,"r"); - if (infile == NULL) error->one(FLERR,"Fix orient/bcc file open failed"); + FILE *inpfile = fopen(xifilename,"r"); + if (inpfile == NULL) error->one(FLERR,"Fix orient/bcc file open failed"); for (int i = 0; i < 4; i++) { - result = fgets(line,IMGMAX,infile); + result = fgets(line,IMGMAX,inpfile); if (!result) error->one(FLERR,"Fix orient/bcc file read failed"); count = sscanf(line,"%lg %lg %lg",&Rxi[i][0],&Rxi[i][1],&Rxi[i][2]); if (count != 3) error->one(FLERR,"Fix orient/bcc file read failed"); } - fclose(infile); + fclose(inpfile); - infile = fopen(chifilename,"r"); - if (infile == NULL) error->one(FLERR,"Fix orient/bcc file open failed"); + inpfile = fopen(chifilename,"r"); + if (inpfile == NULL) error->one(FLERR,"Fix orient/bcc file open failed"); for (int i = 0; i < 4; i++) { - result = fgets(line,IMGMAX,infile); + result = fgets(line,IMGMAX,inpfile); if (!result) error->one(FLERR,"Fix orient/bcc file read failed"); count = sscanf(line,"%lg %lg %lg",&Rchi[i][0],&Rchi[i][1],&Rchi[i][2]); if (count != 3) error->one(FLERR,"Fix orient/bcc file read failed"); } - fclose(infile); + fclose(inpfile); } MPI_Bcast(&Rxi[0][0],18,MPI_DOUBLE,0,world); diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index 5b394adde7..fc827ceb8f 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -113,25 +113,25 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) : char *result; int count; - FILE *infile = fopen(xifilename,"r"); - if (infile == NULL) error->one(FLERR,"Fix orient/fcc file open failed"); + FILE *inpfile = fopen(xifilename,"r"); + if (inpfile == NULL) error->one(FLERR,"Fix orient/fcc file open failed"); for (int i = 0; i < 6; i++) { - result = fgets(line,IMGMAX,infile); + result = fgets(line,IMGMAX,inpfile); if (!result) error->one(FLERR,"Fix orient/fcc file read failed"); count = sscanf(line,"%lg %lg %lg",&Rxi[i][0],&Rxi[i][1],&Rxi[i][2]); if (count != 3) error->one(FLERR,"Fix orient/fcc file read failed"); } - fclose(infile); + fclose(inpfile); - infile = fopen(chifilename,"r"); - if (infile == NULL) error->one(FLERR,"Fix orient/fcc file open failed"); + inpfile = fopen(chifilename,"r"); + if (inpfile == NULL) error->one(FLERR,"Fix orient/fcc file open failed"); for (int i = 0; i < 6; i++) { - result = fgets(line,IMGMAX,infile); + result = fgets(line,IMGMAX,inpfile); if (!result) error->one(FLERR,"Fix orient/fcc file read failed"); count = sscanf(line,"%lg %lg %lg",&Rchi[i][0],&Rchi[i][1],&Rchi[i][2]); if (count != 3) error->one(FLERR,"Fix orient/fcc file read failed"); } - fclose(infile); + fclose(inpfile); } MPI_Bcast(&Rxi[0][0],18,MPI_DOUBLE,0,world); diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 3963379356..6b68c52dbb 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -146,12 +146,12 @@ void NEB::command(int narg, char **arg) if (strcmp(arg[5],"final") == 0) { if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB command"); - infile = arg[6]; - readfile(infile,0); + inpfile = arg[6]; + readfile(inpfile,0); } else if (strcmp(arg[5],"each") == 0) { if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB command"); - infile = arg[6]; - readfile(infile,1); + inpfile = arg[6]; + readfile(inpfile,1); } else if (strcmp(arg[5],"none") == 0) { if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEB command"); } else error->universe_all(FLERR,"Illegal NEB command"); diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index 9453c3c43b..f585a0c8a7 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -47,7 +47,7 @@ class NEB : protected Pointers { double ftol; // force tolerance convergence criterion int n1steps, n2steps; // number of steps in stage 1 and 2 int nevery; // output interval - char *infile; // name of file containing final state + char *inpfile; // name of file containing final state class FixNEB *fneb; int numall; // per-replica dimension of array all diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 8fa43b89ce..abb669bc02 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -59,7 +59,7 @@ enum{ISO,ANISO,TRICLINIC}; FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), step_respa(NULL), - infile(NULL), nrigid(NULL), mol2body(NULL), body2mol(NULL), + inpfile(NULL), nrigid(NULL), mol2body(NULL), body2mol(NULL), body(NULL), displace(NULL), masstotal(NULL), xcm(NULL), vcm(NULL), fcm(NULL), inertia(NULL), ex_space(NULL), ey_space(NULL), ez_space(NULL), angmom(NULL), omega(NULL), @@ -327,7 +327,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : t_iter = 1; t_order = 3; p_chain = 10; - infile = NULL; + inpfile = NULL; pcouple = NONE; pstyle = ANISO; @@ -546,12 +546,12 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : p_chain = force->inumeric(FLERR,arg[iarg+1]); iarg += 2; - } else if (strcmp(arg[iarg],"infile") == 0) { + } else if (strcmp(arg[iarg],"inpfile") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command"); - delete [] infile; + delete [] inpfile; int n = strlen(arg[iarg+1]) + 1; - infile = new char[n]; - strcpy(infile,arg[iarg+1]); + inpfile = new char[n]; + strcpy(inpfile,arg[iarg+1]); restart_file = 1; reinitflag = 0; iarg += 2; @@ -649,7 +649,7 @@ FixRigid::~FixRigid() atom->delete_callback(id,0); delete random; - delete [] infile; + delete [] inpfile; memory->destroy(mol2body); memory->destroy(body2mol); @@ -760,14 +760,14 @@ void FixRigid::init() // setup rigid bodies, using current atom info. if reinitflag is not set, // do the initialization only once, b/c properties may not be re-computable // especially if overlapping particles. - // do not do dynamic init if read body properties from infile. - // this is b/c the infile defines the static and dynamic properties and may + // do not do dynamic init if read body properties from inpfile. + // this is b/c the inpfile defines the static and dynamic properties and may // not be computable if contain overlapping particles. - // setup_bodies_static() reads infile itself + // setup_bodies_static() reads inpfile itself if (reinitflag || !setupflag) { setup_bodies_static(); - if (!infile) setup_bodies_dynamic(); + if (!inpfile) setup_bodies_dynamic(); setupflag = 1; } @@ -1640,7 +1640,7 @@ void FixRigid::set_v() sets extended flags, masstotal, center-of-mass sets Cartesian and diagonalized inertia tensor sets body image flags - may read some properties from infile + may read some properties from inpfile ------------------------------------------------------------------------- */ void FixRigid::setup_bodies_static() @@ -1791,7 +1791,7 @@ void FixRigid::setup_bodies_static() xcm[ibody][2] = all[ibody][2]/masstotal[ibody]; } - // set vcm, angmom = 0.0 in case infile is used + // set vcm, angmom = 0.0 in case inpfile is used // and doesn't overwrite all body's values // since setup_bodies_dynamic() will not be called @@ -1810,7 +1810,7 @@ void FixRigid::setup_bodies_static() // inbody[i] = 0/1 if Ith rigid body is initialized by file int *inbody; - if (infile) { + if (inpfile) { memory->create(inbody,nbody,"rigid:inbody"); for (ibody = 0; ibody < nbody; ibody++) inbody[ibody] = 0; readfile(0,masstotal,xcm,vcm,angmom,imagebody,inbody); @@ -1918,7 +1918,7 @@ void FixRigid::setup_bodies_static() // overwrite Cartesian inertia tensor with file values - if (infile) readfile(1,NULL,all,NULL,NULL,NULL,inbody); + if (inpfile) readfile(1,NULL,all,NULL,NULL,NULL,inbody); // diagonalize inertia tensor for each body via Jacobi rotations // inertia = 3 eigenvalues = principal moments of inertia @@ -2116,11 +2116,11 @@ void FixRigid::setup_bodies_static() MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world); // error check that re-computed moments of inertia match diagonalized ones - // do not do test for bodies with params read from infile + // do not do test for bodies with params read from inpfile double norm; for (ibody = 0; ibody < nbody; ibody++) { - if (infile && inbody[ibody]) continue; + if (inpfile && inbody[ibody]) continue; if (inertia[ibody][0] == 0.0) { if (fabs(all[ibody][0]) > TOLERANCE) error->all(FLERR,"Fix rigid: Bad principal moments"); @@ -2149,7 +2149,7 @@ void FixRigid::setup_bodies_static() error->all(FLERR,"Fix rigid: Bad principal moments"); } - if (infile) memory->destroy(inbody); + if (inpfile) memory->destroy(inbody); } /* ---------------------------------------------------------------------- @@ -2268,10 +2268,10 @@ void FixRigid::readfile(int which, double *vec, char line[MAXLINE]; if (me == 0) { - fp = fopen(infile,"r"); + fp = fopen(inpfile,"r"); if (fp == NULL) { char str[128]; - snprintf(str,128,"Cannot open fix rigid infile %s",infile); + snprintf(str,128,"Cannot open fix rigid inpfile %s",inpfile); error->one(FLERR,str); } @@ -2371,7 +2371,7 @@ void FixRigid::readfile(int which, double *vec, /* ---------------------------------------------------------------------- write out restart info for mass, COM, inertia tensor, image flags to file - identical format to infile option, so info can be read in when restarting + identical format to inpfile option, so info can be read in when restarting only proc 0 writes list of global bodies to file ------------------------------------------------------------------------- */ diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h index 507e4c7553..d9d7b07ce8 100644 --- a/src/RIGID/fix_rigid.h +++ b/src/RIGID/fix_rigid.h @@ -67,7 +67,7 @@ class FixRigid : public Fix { int triclinic; double MINUSPI,TWOPI; - char *infile; // file to read rigid body attributes from + char *inpfile; // file to read rigid body attributes from int rstyle; // SINGLE,MOLECULE,GROUP int setupflag; // 1 if body properties are setup, else 0 int earlyflag; // 1 if forces/torques computed at post_force() @@ -261,7 +261,7 @@ E: Fix rigid: Bad principal moments The principal moments of inertia computed for a rigid body are not within the required tolerances. -E: Cannot open fix rigid infile %s +E: Cannot open fix rigid inpfile %s The specified file cannot be opened. Check that the path and name are correct. diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 54fb83f0aa..dedd71c98d 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -70,7 +70,7 @@ enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF}; FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), step_respa(NULL), - infile(NULL), body(NULL), bodyown(NULL), bodytag(NULL), atom2body(NULL), + inpfile(NULL), body(NULL), bodyown(NULL), bodytag(NULL), atom2body(NULL), xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL), avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL), itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL), @@ -191,7 +191,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : int seed; langflag = 0; - infile = NULL; + inpfile = NULL; onemols = NULL; reinitflag = 1; @@ -232,12 +232,12 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : if (seed <= 0) error->all(FLERR,"Illegal fix rigid/small command"); iarg += 5; - } else if (strcmp(arg[iarg],"infile") == 0) { + } else if (strcmp(arg[iarg],"inpfile") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command"); - delete [] infile; + delete [] inpfile; int n = strlen(arg[iarg+1]) + 1; - infile = new char[n]; - strcpy(infile,arg[iarg+1]); + inpfile = new char[n]; + strcpy(inpfile,arg[iarg+1]); restart_file = 1; reinitflag = 0; iarg += 2; @@ -546,7 +546,7 @@ FixRigidSmall::~FixRigidSmall() memory->destroy(dorient); delete random; - delete [] infile; + delete [] inpfile; memory->destroy(langextra); memory->destroy(mass_body); @@ -622,10 +622,10 @@ void FixRigidSmall::init() if reinitflag is not set, do the initialization only once, b/c properties may not be re-computable especially if overlapping particles or bodies are inserted from mol template. - do not do dynamic init if read body properties from infile. this - is b/c the infile defines the static and dynamic properties and may not + do not do dynamic init if read body properties from inpfile. this + is b/c the inpfile defines the static and dynamic properties and may not be computable if contain overlapping particles setup_bodies_static() - reads infile itself. + reads inpfile itself. cannot do this until now, b/c requires comm->setup() to have setup stencil invoke pre_neighbor() to insure body xcmimage flags are reset needed if Verlet::setup::pbc() has remapped/migrated atoms for 2nd run @@ -638,7 +638,7 @@ void FixRigidSmall::setup_pre_neighbor() setup_bodies_static(); else pre_neighbor(); - if ((reinitflag || !setupflag) && !infile) + if ((reinitflag || !setupflag) && !inpfile) setup_bodies_dynamic(); setupflag = 1; @@ -1775,7 +1775,7 @@ int FixRigidSmall::rendezvous_body(int n, char *inbuf, sets extended flags, masstotal, center-of-mass sets Cartesian and diagonalized inertia tensor sets body image flags - may read some properties from infile + may read some properties from inpfile ------------------------------------------------------------------------- */ void FixRigidSmall::setup_bodies_static() @@ -1932,7 +1932,7 @@ void FixRigidSmall::setup_bodies_static() xcm[2] /= body[ibody].mass; } - // set vcm, angmom = 0.0 in case infile is used + // set vcm, angmom = 0.0 in case inpfile is used // and doesn't overwrite all body's values // since setup_bodies_dynamic() will not be called @@ -1955,7 +1955,7 @@ void FixRigidSmall::setup_bodies_static() // inbody[i] = 0/1 if Ith rigid body is initialized by file int *inbody; - if (infile) { + if (inpfile) { memory->create(inbody,nlocal_body,"rigid/small:inbody"); for (ibody = 0; ibody < nlocal_body; ibody++) inbody[ibody] = 0; readfile(0,NULL,inbody); @@ -2058,7 +2058,7 @@ void FixRigidSmall::setup_bodies_static() // overwrite Cartesian inertia tensor with file values - if (infile) readfile(1,itensor,inbody); + if (inpfile) readfile(1,itensor,inbody); // diagonalize inertia tensor for each body via Jacobi rotations // inertia = 3 eigenvalues = principal moments of inertia @@ -2257,11 +2257,11 @@ void FixRigidSmall::setup_bodies_static() comm->reverse_comm_fix(this,6); // error check that re-computed moments of inertia match diagonalized ones - // do not do test for bodies with params read from infile + // do not do test for bodies with params read from inpfile double norm; for (ibody = 0; ibody < nlocal_body; ibody++) { - if (infile && inbody[ibody]) continue; + if (inpfile && inbody[ibody]) continue; inertia = body[ibody].inertia; if (inertia[0] == 0.0) { @@ -2295,7 +2295,7 @@ void FixRigidSmall::setup_bodies_static() // clean up memory->destroy(itensor); - if (infile) memory->destroy(inbody); + if (inpfile) memory->destroy(inbody); } /* ---------------------------------------------------------------------- @@ -2437,10 +2437,10 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody) // open file and read header if (me == 0) { - fp = fopen(infile,"r"); + fp = fopen(inpfile,"r"); if (fp == NULL) { char str[128]; - snprintf(str,128,"Cannot open fix rigid/small infile %s",infile); + snprintf(str,128,"Cannot open fix rigid/small inpfile %s",inpfile); error->one(FLERR,str); } @@ -2538,7 +2538,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody) /* ---------------------------------------------------------------------- write out restart info for mass, COM, inertia tensor to file - identical format to infile option, so info can be read in when restarting + identical format to inpfile option, so info can be read in when restarting each proc contributes info for rigid bodies it owns ------------------------------------------------------------------------- */ diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h index b5a3d5208d..6dae443d1c 100644 --- a/src/RIGID/fix_rigid_small.h +++ b/src/RIGID/fix_rigid_small.h @@ -74,7 +74,7 @@ class FixRigidSmall : public Fix { int triclinic; double MINUSPI,TWOPI; - char *infile; // file to read rigid body attributes from + char *inpfile; // file to read rigid body attributes from int setupflag; // 1 if body properties are setup, else 0 int earlyflag; // 1 if forces/torques are computed at post_force() int commflag; // various modes of forward/reverse comm @@ -318,7 +318,7 @@ E: Fix rigid: Bad principal moments The principal moments of inertia computed for a rigid body are not within the required tolerances. -E: Cannot open fix rigid/small infile %s +E: Cannot open fix rigid/small inpfile %s The specified file cannot be opened. Check that the path and name are correct. diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 126cfb09e3..46a0541488 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -139,12 +139,12 @@ void NEBSpin::command(int narg, char **arg) if (strcmp(arg[5],"final") == 0) { if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command"); - infile = arg[6]; - readfile(infile,0); + inpfile = arg[6]; + readfile(inpfile,0); } else if (strcmp(arg[5],"each") == 0) { if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command"); - infile = arg[6]; - readfile(infile,1); + inpfile = arg[6]; + readfile(inpfile,1); } else if (strcmp(arg[5],"none") == 0) { if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEBSpin command"); } else error->universe_all(FLERR,"Illegal NEBSpin command"); diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index 5acd034e95..c128eaffa4 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -46,7 +46,7 @@ class NEBSpin : protected Pointers { double ttol; // torque tolerance convergence criterion int n1steps, n2steps; // number of steps in stage 1 and 2 int nevery; // output interval - char *infile; // name of file containing final state + char *inpfile; // name of file containing final state class FixNEBSpin *fneb; int numall; // per-replica dimension of array all diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 5aa4622a67..6e156da837 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -580,32 +580,32 @@ void ReadRestart::command(int narg, char **arg) } /* ---------------------------------------------------------------------- - infile contains a "*" - search for all files which match the infile pattern + inpfile contains a "*" + search for all files which match the inpfile pattern replace "*" with latest timestep value to create outfile name search dir referenced by initial pathname of file - if infile also contains "%", use "base" when searching directory + if inpfile also contains "%", use "base" when searching directory only called by proc 0 ------------------------------------------------------------------------- */ -void ReadRestart::file_search(char *infile, char *outfile) +void ReadRestart::file_search(char *inpfile, char *outfile) { char *ptr; - // separate infile into dir + filename + // separate inpfile into dir + filename - char *dirname = new char[strlen(infile) + 1]; - char *filename = new char[strlen(infile) + 1]; + char *dirname = new char[strlen(inpfile) + 1]; + char *filename = new char[strlen(inpfile) + 1]; - if (strchr(infile,'/')) { - ptr = strrchr(infile,'/'); + if (strchr(inpfile,'/')) { + ptr = strrchr(inpfile,'/'); *ptr = '\0'; - strcpy(dirname,infile); + strcpy(dirname,inpfile); strcpy(filename,ptr+1); *ptr = '/'; } else { strcpy(dirname,"./"); - strcpy(filename,infile); + strcpy(filename,inpfile); } // if filename contains "%" replace "%" with "base" @@ -651,11 +651,11 @@ void ReadRestart::file_search(char *infile, char *outfile) if (maxnum < 0) error->one(FLERR,"Found no restart file matching pattern"); // create outfile with maxint substituted for "*" - // use original infile, not pattern, since need to retain "%" in filename + // use original inpfile, not pattern, since need to retain "%" in filename - ptr = strchr(infile,'*'); + ptr = strchr(inpfile,'*'); *ptr = '\0'; - sprintf(outfile,"%s" BIGINT_FORMAT "%s",infile,maxnum,ptr+1); + sprintf(outfile,"%s" BIGINT_FORMAT "%s",inpfile,maxnum,ptr+1); *ptr = '*'; // clean up