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use scoped enums from Dump and Thermo classes instead of replicating them, reformat

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This commit is contained in:
Axel Kohlmeyer
2021-07-18 17:44:06 -04:00
parent 2eff15d1e6
commit ce7cca2ae4
1 changed files with 46 additions and 81 deletions
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127
src/NETCDF/dump_netcdf.cpp
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@ -44,9 +44,6 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace MathConst; using namespace MathConst;
enum{THERMO_INT,THERMO_FLOAT,THERMO_BIGINT}; // same as in thermo.cpp
enum{DUMP_INT,DUMP_DOUBLE,DUMP_STRING,DUMP_BIGINT}; // same as in DumpCFG
static const char NC_FRAME_STR[] = "frame"; static const char NC_FRAME_STR[] = "frame";
static const char NC_SPATIAL_STR[] = "spatial"; static const char NC_SPATIAL_STR[] = "spatial";
static const char NC_VOIGT_STR[] = "Voigt"; static const char NC_VOIGT_STR[] = "Voigt";
@ -60,8 +57,8 @@ static const char NC_CELL_ORIGIN_STR[] = "cell_origin";
static const char NC_CELL_LENGTHS_STR[] = "cell_lengths"; static const char NC_CELL_LENGTHS_STR[] = "cell_lengths";
static const char NC_CELL_ANGLES_STR[] = "cell_angles"; static const char NC_CELL_ANGLES_STR[] = "cell_angles";
const char NC_UNITS_STR[] = "units"; static const char NC_UNITS_STR[] = "units";
const char NC_SCALE_FACTOR_STR[] = "scale_factor"; static const char NC_SCALE_FACTOR_STR[] = "scale_factor";
static constexpr int THIS_IS_A_FIX = -1; static constexpr int THIS_IS_A_FIX = -1;
static constexpr int THIS_IS_A_COMPUTE = -2; static constexpr int THIS_IS_A_COMPUTE = -2;
@ -400,9 +397,9 @@ void DumpNetCDF::openfile()
nc_type xtype; nc_type xtype;
// Type mangling // Type mangling
if (vtype[perat[i].field[0]] == DUMP_INT) { if (vtype[perat[i].field[0]] == Dump::INT) {
xtype = NC_INT; xtype = NC_INT;
} else if (vtype[perat[i].field[0]] == DUMP_BIGINT) { } else if (vtype[perat[i].field[0]] == Dump::BIGINT) {
xtype = NC_INT64; xtype = NC_INT64;
} else { } else {
if (double_precision) if (double_precision)
@ -435,13 +432,13 @@ void DumpNetCDF::openfile()
if (thermo) { if (thermo) {
Thermo *th = output->thermo; Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) { for (int i = 0; i < th->nfield; i++) {
if (th->vtype[i] == THERMO_FLOAT) { if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( nc_def_var(ncid, th->keyword[i], NC_DOUBLE, 1, dims, NCERRX( nc_def_var(ncid, th->keyword[i], NC_DOUBLE, 1, dims,
&thermovar[i]), th->keyword[i] ); &thermovar[i]), th->keyword[i] );
} else if (th->vtype[i] == THERMO_INT) { } else if (th->vtype[i] == Thermo::INT) {
NCERRX( nc_def_var(ncid, th->keyword[i], NC_INT, 1, dims, NCERRX( nc_def_var(ncid, th->keyword[i], NC_INT, 1, dims,
&thermovar[i]), th->keyword[i] ); &thermovar[i]), th->keyword[i] );
} else if (th->vtype[i] == THERMO_BIGINT) { } else if (th->vtype[i] == Thermo::BIGINT) {
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG) #if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
NCERRX( nc_def_var(ncid, th->keyword[i], NC_INT64, 1, dims, NCERRX( nc_def_var(ncid, th->keyword[i], NC_INT64, 1, dims,
&thermovar[i]), th->keyword[i] ); &thermovar[i]), th->keyword[i] );
@ -454,77 +451,50 @@ void DumpNetCDF::openfile()
} }
// attributes // attributes
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "Conventions", NCERR( nc_put_att_text(ncid, NC_GLOBAL, "Conventions",5, "AMBER") );
5, "AMBER") ); NCERR( nc_put_att_text(ncid, NC_GLOBAL, "ConventionVersion",3, "1.0") );
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "ConventionVersion",
3, "1.0") );
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "program", NCERR( nc_put_att_text(ncid, NC_GLOBAL, "program",6, "LAMMPS") );
6, "LAMMPS") ); NCERR( nc_put_att_text(ncid, NC_GLOBAL, "programVersion",strlen(lmp->version), lmp->version) );
NCERR( nc_put_att_text(ncid, NC_GLOBAL, "programVersion",
strlen(lmp->version), lmp->version) );
// units // units
if (!strcmp(update->unit_style, "lj")) { if (!strcmp(update->unit_style, "lj")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,2, "lj") );
2, "lj") ); NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,2, "lj") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,2, "lj") );
2, "lj") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
2, "lj") );
} else if (!strcmp(update->unit_style, "real")) { } else if (!strcmp(update->unit_style, "real")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,11, "femtosecond") );
11, "femtosecond") ); NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,8, "Angstrom") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,8, "Angstrom") );
8, "Angstrom") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
8, "Angstrom") );
} else if (!strcmp(update->unit_style, "metal")) { } else if (!strcmp(update->unit_style, "metal")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,10, "picosecond") );
10, "picosecond") ); NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,8, "Angstrom") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,8, "Angstrom") );
8, "Angstrom") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
8, "Angstrom") );
} else if (!strcmp(update->unit_style, "si")) { } else if (!strcmp(update->unit_style, "si")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,6, "second") );
6, "second") ); NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,5, "meter") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,5, "meter") );
5, "meter") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
5, "meter") );
} else if (!strcmp(update->unit_style, "cgs")) { } else if (!strcmp(update->unit_style, "cgs")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,6, "second") );
6, "second") ); NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,10, "centimeter") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,10, "centimeter") );
10, "centimeter") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
10, "centimeter") );
} else if (!strcmp(update->unit_style, "electron")) { } else if (!strcmp(update->unit_style, "electron")) {
NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, time_var, NC_UNITS_STR,11, "femtosecond") );
11, "femtosecond") ); NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR,4, "Bohr") );
NCERR( nc_put_att_text(ncid, cell_origin_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,4, "Bohr") );
4, "Bohr") );
NCERR( nc_put_att_text(ncid, cell_lengths_var, NC_UNITS_STR,
4, "Bohr") );
} else { } else {
char errstr[1024]; char errstr[1024];
sprintf(errstr, "Unsupported unit style '%s'", update->unit_style); error->all(FLERR,"Unsupported unit style '{}", update->unit_style);
error->all(FLERR,errstr);
} }
NCERR( nc_put_att_text(ncid, cell_angles_var, NC_UNITS_STR, NCERR( nc_put_att_text(ncid, cell_angles_var, NC_UNITS_STR,6, "degree") );
6, "degree") );
d[0] = update->dt; d[0] = update->dt;
NCERR( nc_put_att_double(ncid, time_var, NC_SCALE_FACTOR_STR, NCERR( nc_put_att_double(ncid, time_var, NC_SCALE_FACTOR_STR,NC_DOUBLE, 1, d) );
NC_DOUBLE, 1, d) );
d[0] = 1.0; d[0] = 1.0;
NCERR( nc_put_att_double(ncid, cell_origin_var, NC_SCALE_FACTOR_STR, NCERR( nc_put_att_double(ncid, cell_origin_var, NC_SCALE_FACTOR_STR,NC_DOUBLE, 1, d) );
NC_DOUBLE, 1, d) );
d[0] = 1.0; d[0] = 1.0;
NCERR( nc_put_att_double(ncid, cell_lengths_var, NC_SCALE_FACTOR_STR, NCERR( nc_put_att_double(ncid, cell_lengths_var, NC_SCALE_FACTOR_STR,NC_DOUBLE, 1, d) );
NC_DOUBLE, 1, d) );
/* /*
* Finished with definition * Finished with definition
@ -663,14 +633,14 @@ void DumpNetCDF::write()
for (int i = 0; i < th->nfield; i++) { for (int i = 0; i < th->nfield; i++) {
th->call_vfunc(i); th->call_vfunc(i);
if (filewriter) { if (filewriter) {
if (th->vtype[i] == THERMO_FLOAT) { if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( nc_put_var1_double(ncid, thermovar[i], start, NCERRX( nc_put_var1_double(ncid, thermovar[i], start,
&th->dvalue), &th->dvalue),
th->keyword[i] ); th->keyword[i] );
} else if (th->vtype[i] == THERMO_INT) { } else if (th->vtype[i] == Thermo::INT) {
NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->ivalue), NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
th->keyword[i] ); th->keyword[i] );
} else if (th->vtype[i] == THERMO_BIGINT) { } else if (th->vtype[i] == Thermo::BIGINT) {
NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue), NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
th->keyword[i] ); th->keyword[i] );
} }
@ -799,7 +769,7 @@ void DumpNetCDF::write_data(int n, double *mybuf)
for (int i = 0; i < n_perat; i++) { for (int i = 0; i < n_perat; i++) {
int iaux = perat[i].field[0]; int iaux = perat[i].field[0];
if (vtype[iaux] == DUMP_INT || vtype[iaux] == DUMP_BIGINT) { if (vtype[iaux] == Dump::INT || vtype[iaux] == Dump::BIGINT) {
// integers // integers
if (perat[i].dims > 1) { if (perat[i].dims > 1) {
@ -807,11 +777,11 @@ void DumpNetCDF::write_data(int n, double *mybuf)
iaux = perat[i].field[idim]; iaux = perat[i].field[idim];
if (iaux >= 0) { if (iaux >= 0) {
if (vtype[iaux] == DUMP_INT) { if (vtype[iaux] == Dump::INT) {
for (int j = 0; j < n; j++, iaux+=size_one) { for (int j = 0; j < n; j++, iaux+=size_one) {
int_buffer[j] = static_cast<int>(mybuf[iaux]); int_buffer[j] = static_cast<int>(mybuf[iaux]);
} }
} else { // DUMP_BIGINT } else { // Dump::BIGINT
for (int j = 0; j < n; j++, iaux+=size_one) { for (int j = 0; j < n; j++, iaux+=size_one) {
int_buffer[j] = static_cast<bigint>(mybuf[iaux]); int_buffer[j] = static_cast<bigint>(mybuf[iaux]);
} }
@ -821,22 +791,19 @@ void DumpNetCDF::write_data(int n, double *mybuf)
if (perat[i].constant) { if (perat[i].constant) {
if (perat[i].ndumped < ntotalgr) { if (perat[i].ndumped < ntotalgr) {
NCERR( nc_put_vars_bigint(ncid, perat[i].var, NCERR( nc_put_vars_bigint(ncid, perat[i].var,start+1, count+1, stride+1,int_buffer) );
start+1, count+1, stride+1,
int_buffer) );
perat[i].ndumped += n; perat[i].ndumped += n;
} }
} else } else
NCERR( nc_put_vars_bigint(ncid, perat[i].var, start, count, stride, NCERR( nc_put_vars_bigint(ncid, perat[i].var, start, count, stride,int_buffer) );
int_buffer) );
} }
} }
} else { } else {
if (vtype[iaux] == DUMP_INT) { if (vtype[iaux] == Dump::INT) {
for (int j = 0; j < n; j++, iaux+=size_one) { for (int j = 0; j < n; j++, iaux+=size_one) {
int_buffer[j] = static_cast<int>(mybuf[iaux]); int_buffer[j] = static_cast<int>(mybuf[iaux]);
} }
} else { // DUMP_BIGINT } else { // Dump::BIGINT
for (int j = 0; j < n; j++, iaux+=size_one) { for (int j = 0; j < n; j++, iaux+=size_one) {
int_buffer[j] = static_cast<bigint>(mybuf[iaux]); int_buffer[j] = static_cast<bigint>(mybuf[iaux]);
} }
@ -844,13 +811,11 @@ void DumpNetCDF::write_data(int n, double *mybuf)
if (perat[i].constant) { if (perat[i].constant) {
if (perat[i].ndumped < ntotalgr) { if (perat[i].ndumped < ntotalgr) {
NCERR( nc_put_vara_bigint(ncid, perat[i].var, start+1, count+1, NCERR( nc_put_vara_bigint(ncid, perat[i].var, start+1, count+1,int_buffer) );
int_buffer) );
perat[i].ndumped += n; perat[i].ndumped += n;
} }
} else } else
NCERR( nc_put_vara_bigint(ncid, perat[i].var, start, count, NCERR( nc_put_vara_bigint(ncid, perat[i].var, start, count,int_buffer) );
int_buffer) );
} }
} else { } else {
// doubles // doubles