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more reformatting

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This commit is contained in:
Axel Kohlmeyer
2021-07-18 18:37:27 -04:00
parent 536ba492fb
commit 1f9e0adfe9
1 changed files with 29 additions and 36 deletions
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65
src/NETCDF/dump_netcdf.cpp
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@ -196,7 +196,7 @@ DumpNetCDF::~DumpNetCDF()
closefile();
delete[] perat;
if (thermovar) delete[] thermovar;
if (thermovar) delete[] thermovar;
if (int_buffer) memory->sfree(int_buffer);
if (double_buffer) memory->sfree(double_buffer);
@ -213,8 +213,7 @@ void DumpNetCDF::openfile()
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s", filestar,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
@ -276,8 +275,7 @@ void DumpNetCDF::openfile()
// Fixme! Perform checks if dimensions and variables conform with
// data structure standard.
if (not utils::file_is_readable(filecurrent))
error->all(FLERR, "cannot append to non-existent file {}",
filecurrent);
error->all(FLERR, "cannot append to non-existent file {}",filecurrent);
if (singlefile_opened) return;
singlefile_opened = 1;
@ -303,8 +301,7 @@ void DumpNetCDF::openfile()
sprintf(dimstr, "vec%i", dims);
}
if (dims != 1) {
NCERRX( nc_inq_dimid(ncid, dimstr, &vector_dim[dims]),
dimstr );
NCERRX( nc_inq_dimid(ncid, dimstr, &vector_dim[dims]), dimstr );
}
}
}
@ -458,40 +455,39 @@ void DumpNetCDF::openfile()
}
// attributes
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "Conventions",5, "AMBER") );
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "ConventionVersion",3, "1.0") );
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "Conventions", 5, "AMBER") );
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "ConventionVersion", 3, "1.0") );
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "program",6, "LAMMPS") );
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "program", 6, "LAMMPS") );
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "programVersion",strlen(lmp->version), lmp->version) );
// units
if (!strcmp(update->unit_style, "lj")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,2, "lj") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,2, "lj") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,2, "lj") );
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 2, "lj") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 2, "lj") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 2, "lj") );
} else if (!strcmp(update->unit_style, "real")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,11, "femtosecond") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,8, "Angstrom") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,8, "Angstrom") );
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 11, "femtosecond") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 8, "Angstrom") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 8, "Angstrom") );
} else if (!strcmp(update->unit_style, "metal")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,10, "picosecond") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,8, "Angstrom") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,8, "Angstrom") );
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 10, "picosecond") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 8, "Angstrom") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 8, "Angstrom") );
} else if (!strcmp(update->unit_style, "si")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,6, "second") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,5, "meter") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,5, "meter") );
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 6, "second") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 5, "meter") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 5, "meter") );
} else if (!strcmp(update->unit_style, "cgs")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,6, "second") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,10, "centimeter") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,10, "centimeter") );
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 6, "second") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 10, "centimeter") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 10, "centimeter") );
} else if (!strcmp(update->unit_style, "electron")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,11, "femtosecond") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,4, "Bohr") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,4, "Bohr") );
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, 11, "femtosecond") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, 4, "Bohr") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR, 4, "Bohr") );
} else {
char errstr[1024];
error->all(FLERR,"Unsupported unit style '{}", update->unit_style);
error->all(FLERR,"Unsupported unit style: {}", update->unit_style);
}
NCERR( nc_put_att_text(ncid, cell_angles_var, NC_UNITS_STR,6, "degree") );
@ -722,12 +718,9 @@ void DumpNetCDF::write_header(bigint n)
count[0] = 1;
count[1] = 3;
NCERR( nc_put_var1_double(ncid, time_var, start, &time) );
NCERR( nc_put_vara_double(ncid, cell_origin_var, start, count,
cell_origin) );
NCERR( nc_put_vara_double(ncid, cell_lengths_var, start, count,
cell_lengths) );
NCERR( nc_put_vara_double(ncid, cell_angles_var, start, count,
cell_angles) );
NCERR( nc_put_vara_double(ncid, cell_origin_var, start, count, cell_origin) );
NCERR( nc_put_vara_double(ncid, cell_lengths_var, start, count, cell_lengths) );
NCERR( nc_put_vara_double(ncid, cell_angles_var, start, count, cell_angles) );
}
ndata = n;