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first stab at implementing dump_modify colname

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This commit is contained in:
Axel Kohlmeyer
2022-04-01 07:41:13 -04:00
parent 4042a52db1
commit ce67cb0ca1
8 changed files with 115 additions and 56 deletions
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66
src/dump.cpp
View File

@ -150,19 +150,19 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
Dump::~Dump()
{
delete [] id;
delete [] style;
delete [] filename;
delete [] multiname;
delete[] id;
delete[] style;
delete[] filename;
delete[] multiname;
delete [] format;
delete [] format_default;
delete [] format_line_user;
delete [] format_float_user;
delete [] format_int_user;
delete [] format_bigint_user;
delete[] format;
delete[] format_default;
delete[] format_line_user;
delete[] format_float_user;
delete[] format_int_user;
delete[] format_bigint_user;
delete [] refresh;
delete[] refresh;
// format_column_user is deallocated by child classes that use it
@ -1019,7 +1019,7 @@ void Dump::balance()
memory->destroy(tmp);
memory->destroy(proc_offsets);
memory->destroy(proc_new_offsets);
delete [] request;
delete[] request;
}
/* ----------------------------------------------------------------------
@ -1059,7 +1059,7 @@ void Dump::modify_params(int narg, char **arg)
if (strcmp(id,output->dump[idump]->id) == 0) break;
int n;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
delete [] output->var_dump[idump];
delete[] output->var_dump[idump];
output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
n = 0;
} else {
@ -1077,7 +1077,7 @@ void Dump::modify_params(int narg, char **arg)
if (strcmp(id,output->dump[idump]->id) == 0) break;
double delta;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
delete [] output->var_dump[idump];
delete[] output->var_dump[idump];
output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
delta = 0.0;
} else {
@ -1107,7 +1107,7 @@ void Dump::modify_params(int narg, char **arg)
MPI_Comm_free(&clustercomm);
MPI_Comm_split(world,icluster,0,&clustercomm);
delete [] multiname;
delete[] multiname;
char *ptr = strchr(filename,'%');
*ptr = '\0';
multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));
@ -1124,14 +1124,38 @@ void Dump::modify_params(int narg, char **arg)
flush_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"colname") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"default") == 0) {
for (auto item : keyword_user) item.clear();
iarg += 2;
} else {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
int icol = -1;
if (utils::is_integer(arg[iarg + 1])) {
icol = utils::inumeric(FLERR,arg[iarg + 1],false,lmp);
if (icol < 0) icol = keyword_user.size() + icol + 1;
icol--;
} else {
try {
icol = key2col.at(arg[iarg + 1]);
} catch (std::out_of_range &) {
icol = -1;
}
}
if ((icol < 0) || (icol >= (int)keyword_user.size()))
error->all(FLERR, "Illegal thermo_modify command");
keyword_user[icol] = arg[iarg+2];
iarg += 3;
}
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"none") == 0) {
delete [] format_line_user;
delete [] format_int_user;
delete [] format_bigint_user;
delete [] format_float_user;
delete[] format_line_user;
delete[] format_int_user;
delete[] format_bigint_user;
delete[] format_float_user;
format_line_user = nullptr;
format_int_user = nullptr;
format_bigint_user = nullptr;
@ -1146,7 +1170,7 @@ void Dump::modify_params(int narg, char **arg)
if (iarg+3 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"line") == 0) {
delete [] format_line_user;
delete[] format_line_user;
format_line_user = utils::strdup(arg[iarg+2]);
iarg += 3;
} else { // pass other format options to child classes
@ -1204,7 +1228,7 @@ void Dump::modify_params(int narg, char **arg)
MPI_Comm_free(&clustercomm);
MPI_Comm_split(world,icluster,0,&clustercomm);
delete [] multiname;
delete[] multiname;
char *ptr = strchr(filename,'%');
*ptr = '\0';
multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));

4
src/dump.h
View File

@ -16,6 +16,8 @@
#include "pointers.h" // IWYU pragma: export
#include <map>
namespace LAMMPS_NS {
class Dump : protected Pointers {
@ -100,6 +102,8 @@ class Dump : protected Pointers {
char *format_bigint_user;
char **format_column_user;
enum { INT, DOUBLE, STRING, BIGINT };
std::map<std::string, int> key2col;
std::vector<std::string> keyword_user;
FILE *fp; // file to write dump to
int size_one; // # of quantities for one atom

29
src/dump_atom.cpp
View File

@ -38,6 +38,9 @@ DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
buffer_allow = 1;
buffer_flag = 1;
format_default = nullptr;
key2col = { { "id", 0 }, { "type", 1 }, { "x", 2 }, { "y", 3 },
{ "z", 4 }, { "ix", 5 }, { "iy", 6 }, { "iz", 7 } };
keyword_user = { "", "", "", "", "", "", "", "" };
}
/* ---------------------------------------------------------------------- */
@ -63,15 +66,25 @@ void DumpAtom::init_style()
domain->boundary_string(boundstr);
// setup column string
std::string default_columns;
if (scale_flag == 0 && image_flag == 0)
columns = (char *) "id type x y z";
default_columns = "id type x y z";
else if (scale_flag == 0 && image_flag == 1)
columns = (char *) "id type x y z ix iy iz";
default_columns = "id type x y z ix iy iz";
else if (scale_flag == 1 && image_flag == 0)
columns = (char *) "id type xs ys zs";
default_columns = "id type xs ys zs";
else if (scale_flag == 1 && image_flag == 1)
columns = (char *) "id type xs ys zs ix iy iz";
default_columns = "id type xs ys zs ix iy iz";
int icol = 0;
columns.clear();
for (auto item : utils::split_words(default_columns)) {
if (columns.size()) columns += " ";
if (keyword_user[icol].size()) columns += keyword_user[icol];
else columns += item;
++icol;
}
// setup function ptrs
@ -201,9 +214,9 @@ void DumpAtom::header_unit_style_binary()
void DumpAtom::header_columns_binary()
{
int len = strlen(columns);
int len = columns.size();
fwrite(&len, sizeof(int), 1, fp);
fwrite(columns, sizeof(char), len, fp);
fwrite(columns.c_str(), sizeof(char), len, fp);
}
/* ---------------------------------------------------------------------- */
@ -301,7 +314,7 @@ void DumpAtom::header_item(bigint ndump)
fprintf(fp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
fprintf(fp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
fprintf(fp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
fprintf(fp,"ITEM: ATOMS %s\n",columns);
fprintf(fp,"ITEM: ATOMS %s\n",columns.c_str());
}
/* ---------------------------------------------------------------------- */
@ -322,7 +335,7 @@ void DumpAtom::header_item_triclinic(bigint ndump)
fprintf(fp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
fprintf(fp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
fprintf(fp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz);
fprintf(fp,"ITEM: ATOMS %s\n",columns);
fprintf(fp,"ITEM: ATOMS %s\n",columns.c_str());
}
/* ---------------------------------------------------------------------- */

2
src/dump_atom.h
View File

@ -36,7 +36,7 @@ class DumpAtom : public Dump {
int scale_flag; // 1 if atom coords are scaled, 0 if no
int image_flag; // 1 if append box count to atom coords, 0 if no
char *columns; // column labels
std::string columns; // column labels
void init_style() override;
int modify_param(int, char **) override;

28
src/dump_cfg.cpp
View File

@ -53,26 +53,26 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(earg[2],"xs") == 0) {
if (strcmp(earg[3],"ysu") == 0 || strcmp(earg[4],"zsu") == 0)
error->all(FLERR,
"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
error->all(FLERR,"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
unwrapflag = 0;
} else {
if (strcmp(earg[3],"ys") == 0 || strcmp(earg[4],"zs") == 0)
error->all(FLERR,
"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
error->all(FLERR,"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
unwrapflag = 1;
}
// setup auxiliary property name strings
// convert 'X_ID[m]' (X=c,f,v) to 'X_ID_m'
if (nfield > 5) auxname = new char*[nfield];
if (nfield > 5) auxname = new char*[nfield-5];
else auxname = nullptr;
int i = 0;
key2col.clear();
keyword_user.resize(nfield-5);
for (int iarg = 5; iarg < nfield; iarg++, i++) {
ArgInfo argi(earg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE
|ArgInfo::DNAME|ArgInfo::INAME);
ArgInfo argi(earg[iarg],ArgInfo::COMPUTE|ArgInfo::FIX|ArgInfo::VARIABLE|
ArgInfo::DNAME|ArgInfo::INAME);
if (argi.get_dim() == 1) {
std::string newarg = fmt::format("{}_{}_{}", earg[iarg][0], argi.get_name(), argi.get_index1());
@ -80,6 +80,8 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
} else {
auxname[i] = utils::strdup(earg[iarg]);
}
key2col[earg[iarg]] = i;
keyword_user[i].clear();
}
}
@ -88,8 +90,8 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
DumpCFG::~DumpCFG()
{
if (auxname) {
for (int i = 0; i < nfield-5; i++) delete [] auxname[i];
delete [] auxname;
for (int i = 0; i < nfield-5; i++) delete[] auxname[i];
delete[] auxname;
}
}
@ -136,8 +138,12 @@ void DumpCFG::write_header(bigint n)
fprintf(fp,"H0(3,3) = %g A\n",domain->zprd);
fprintf(fp,".NO_VELOCITY.\n");
fprintf(fp,"entry_count = %d\n",nfield-2);
for (int i = 0; i < nfield-5; i++)
fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]);
for (int i = 0; i < nfield-5; i++) {
if (keyword_user[i].size())
fprintf(fp,"auxiliary[%d] = %s\n",i,keyword_user[i].c_str());
else
fprintf(fp,"auxiliary[%d] = %s\n",i,auxname[i]);
}
}
/* ----------------------------------------------------------------------

36
src/dump_custom.cpp
View File

@ -55,14 +55,11 @@ enum{LT,LE,GT,GE,EQ,NEQ,XOR};
DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
Dump(lmp, narg, arg),
idregion(nullptr), thresh_array(nullptr), thresh_op(nullptr), thresh_value(nullptr),
thresh_last(nullptr), thresh_fix(nullptr),
thresh_fixID(nullptr), thresh_first(nullptr),
earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr), choose(nullptr),
dchoose(nullptr), clist(nullptr), field2index(nullptr),
argindex(nullptr), id_compute(nullptr),
compute(nullptr), id_fix(nullptr), fix(nullptr),
id_variable(nullptr), variable(nullptr),
vbuf(nullptr), id_custom(nullptr), custom(nullptr), custom_flag(nullptr),
thresh_last(nullptr), thresh_fix(nullptr), thresh_fixID(nullptr), thresh_first(nullptr),
earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr), columns_default(nullptr),
choose(nullptr), dchoose(nullptr), clist(nullptr), field2index(nullptr), argindex(nullptr),
id_compute(nullptr), compute(nullptr), id_fix(nullptr), fix(nullptr), id_variable(nullptr),
variable(nullptr), vbuf(nullptr), id_custom(nullptr), custom(nullptr), custom_flag(nullptr),
typenames(nullptr), pack_choice(nullptr)
{
if (narg == 5) error->all(FLERR,"No dump custom arguments specified");
@ -180,13 +177,14 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
// setup column string
cols.clear();
keyword_user.resize(nfield);
for (int iarg = 0; iarg < nfield; iarg++) {
key2col[earg[iarg]] = iarg;
keyword_user[iarg].clear();
if (cols.size()) cols += " ";
cols += earg[iarg];
cols += " ";
}
// remove trailing blank and copy
cols.resize(cols.size()-1);
columns = utils::strdup(cols);
columns_default = utils::strdup(cols);
}
/* ---------------------------------------------------------------------- */
@ -257,6 +255,7 @@ DumpCustom::~DumpCustom()
delete[] format_column_user;
}
delete[] columns_default;
delete[] columns;
}
@ -264,6 +263,19 @@ DumpCustom::~DumpCustom()
void DumpCustom::init_style()
{
// assemble ITEMS: column string from defaults and user values
delete[] columns;
std::string combined;
int icol = 0;
for (auto item : utils::split_words(columns_default)) {
if (combined.size()) combined += " ";
if (keyword_user[icol].size()) combined += keyword_user[icol];
else combined += item;
++icol;
}
columns = utils::strdup(combined);
// format = copy of default or user-specified line format
delete[] format;

1
src/dump_custom.h
View File

@ -60,6 +60,7 @@ class DumpCustom : public Dump {
char **vformat; // format string for each vector element
//
char *columns; // column labels
char *columns_default;
//
int nchoose; // # of selected atoms
int maxlocal; // size of atom selection and variable arrays

5
src/thermo.cpp
View File

@ -631,8 +631,7 @@ void Thermo::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg], "colname") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal thermo_modify command");
if (strcmp(arg[iarg + 1], "default") == 0) {
for (int i=0; i < nfield_initial + 1; ++i)
keyword_user[i].clear();
for (auto item : keyword_user) item.clear();
iarg += 2;
} else {
if (iarg + 3 > narg) error->all(FLERR, "Illegal thermo_modify command");
@ -660,7 +659,7 @@ void Thermo::modify_params(int narg, char **arg)
format_int_user.clear();
format_bigint_user.clear();
format_float_user.clear();
for (int i = 0; i < nfield_initial + 1; ++i) format_column_user[i].clear();
for (auto item : format_column_user) item.clear();
iarg += 2;
continue;
}