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remove class member name clashes. Pointers contains `infile` so we rename other uses to `inpfile`

This commit is contained in:
Axel Kohlmeyer 2019-06-23 16:43:54 -04:00
parent f190647ab4
commit 171d74f2f2
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
11 changed files with 86 additions and 86 deletions
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16
src/MISC/fix_orient_bcc.cpp
View File

@ -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);

16
src/MISC/fix_orient_fcc.cpp
View File

@ -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);

8
src/REPLICA/neb.cpp
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@ -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");

2
src/REPLICA/neb.h
View File

@ -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

42
src/RIGID/fix_rigid.cpp
View File

@ -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
------------------------------------------------------------------------- */

4
src/RIGID/fix_rigid.h
View File

@ -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.

42
src/RIGID/fix_rigid_small.cpp
View File

@ -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
------------------------------------------------------------------------- */

4
src/RIGID/fix_rigid_small.h
View File

@ -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.

8
src/SPIN/neb_spin.cpp
View File

@ -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");

2
src/SPIN/neb_spin.h
View File

@ -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

28
src/read_restart.cpp
View File

@ -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