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new utility function "utils::expand_type" to convert type labels to numeric strings

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This commit is contained in:
Axel Kohlmeyer
2022-09-05 05:45:31 -04:00
parent e1960bbb9a
commit 75e897b2fe
5 changed files with 91 additions and 5 deletions
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3
doc/src/Developer_utils.rst
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@ -211,6 +211,9 @@ Argument processing
.. doxygenfunction:: expand_args
:project: progguide
.. doxygenfunction:: expand_type
:project: progguide
Convenience functions
^^^^^^^^^^^^^^^^^^^^^

21
src/utils.cpp
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@ -20,6 +20,7 @@
#include "fix.h"
#include "fmt/chrono.h"
#include "input.h"
#include "label_map.h"
#include "memory.h"
#include "modify.h"
#include "text_file_reader.h"
@ -766,6 +767,26 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod
return newarg;
}
/* -------------------------------------------------------------------------
Expand type string to numeric string from labelmap.
Return copy of expanded type or null pointer.
------------------------------------------------------------------------- */
char *utils::expand_type(const char *file, int line, const std::string &str, int mode, LAMMPS *lmp)
{
if (!lmp) return nullptr;
if (is_type(str) == 1) {
if (!lmp->atom->labelmapflag)
lmp->error->all(file, line, "Type string {} cannot be used without a labelmap", str);
int type = lmp->atom->lmap->find(str, mode);
if (type == -1) lmp->error->all(file, line, "Type string {} not found in labelmap", str);
return utils::strdup(std::to_string(type));
} else
return nullptr;
}
/* ----------------------------------------------------------------------
Make copy of string in new storage. Works like the (non-portable)
C-style strdup() but also accepts a C++ string as argument.

18
src/utils.h
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@ -359,6 +359,24 @@ namespace utils {
int expand_args(const char *file, int line, int narg, char **arg, int mode, char **&earg,
LAMMPS *lmp);
/*! Expand type label string into its equivalent numeric type
*
* This function checks if a given string may be a type label and
* then searches the labelmap type indicated by the *mode* argument
* for the corresponding numeric type. If this is found a copy of
* the numeric type string is made and returned. Otherwise a null
* pointer is returned.
* If a string is returned, the calling code must free it with delete[].
*
* \param file name of source file for error message
* \param line line number in source file for error message
* \param str type string to be expanded
* \param mode select labelmap using constants from Atom class
* \param lmp pointer to top-level LAMMPS class instance
* \return pointer to expanded string or null pointer */
char *expand_type(const char *file, int line, const std::string &str, int mode, LAMMPS *lmp);
/*! Make C-style copy of string in new storage
*
* This allocates a storage buffer and copies the C-style or

41
unittest/commands/test_labelmap.cpp
View File

@ -63,6 +63,13 @@ TEST_F(LabelMapTest, Atoms)
BEGIN_HIDE_OUTPUT();
command("region box block 0 2 0 2 0 2");
command("create_box 4 box");
END_HIDE_OUTPUT();
EXPECT_EQ(domain->box_exist, 1);
EXPECT_EQ(atom->lmap, nullptr);
TEST_FAILURE(".*ERROR: Type string C1 cannot be used without a labelmap.*",
utils::expand_type(FLERR, "C1", Atom::ATOM, lmp););
BEGIN_HIDE_OUTPUT();
command("labelmap atom 2 N1");
command("labelmap atom 3 O1 4 H1");
command("mass * 1.0");
@ -89,6 +96,22 @@ TEST_F(LabelMapTest, Atoms)
EXPECT_EQ(atom->lmap->find("X", Atom::ATOM), -1);
EXPECT_DOUBLE_EQ(atom->mass[3], 10.0);
EXPECT_EQ(utils::expand_type(FLERR, "1", Atom::ATOM, lmp), nullptr);
EXPECT_EQ(utils::expand_type(FLERR, "*3", Atom::ATOM, lmp), nullptr);
EXPECT_EQ(utils::expand_type(FLERR, "1*2", Atom::ATOM, lmp), nullptr);
EXPECT_EQ(utils::expand_type(FLERR, "*", Atom::ATOM, lmp), nullptr);
EXPECT_EQ(utils::expand_type(FLERR, "**", Atom::ATOM, lmp), nullptr);
EXPECT_EQ(utils::expand_type(FLERR, "1*2*", Atom::ATOM, lmp), nullptr);
auto expanded = utils::expand_type(FLERR, "C1", Atom::ATOM, lmp);
EXPECT_THAT(expanded, StrEq("1"));
delete[] expanded;
expanded = utils::expand_type(FLERR, "O#", Atom::ATOM, lmp);
EXPECT_THAT(expanded, StrEq("3"));
delete[] expanded;
TEST_FAILURE(".*ERROR: Type string XX not found in labelmap.*",
utils::expand_type(FLERR, "XX", Atom::ATOM, lmp););
TEST_FAILURE(".*ERROR: Labelmap atom type 0 must be within 1-4.*",
command("labelmap atom 0 C1"););
TEST_FAILURE(".*ERROR: Labelmap atom type 5 must be within 1-4.*",
@ -238,6 +261,24 @@ TEST_F(LabelMapTest, Topology)
EXPECT_EQ(atom->lmap->find("X", Atom::ATOM), -1);
EXPECT_EQ(atom->lmap->find("N2'-C1\"-N2'", Atom::BOND), -1);
platform::unlink("labelmap_topology.inc");
auto expanded = utils::expand_type(FLERR, "N2'", Atom::ATOM, lmp);
EXPECT_THAT(expanded, StrEq("2"));
delete[] expanded;
expanded = utils::expand_type(FLERR, "[C1][C1]", Atom::BOND, lmp);
EXPECT_THAT(expanded, StrEq("2"));
delete[] expanded;
expanded = utils::expand_type(FLERR, "C1-N2-C1", Atom::ANGLE, lmp);
EXPECT_THAT(expanded, StrEq("1"));
delete[] expanded;
expanded = utils::expand_type(FLERR, "C1-N2-C1-N2", Atom::DIHEDRAL, lmp);
EXPECT_THAT(expanded, StrEq("1"));
delete[] expanded;
expanded = utils::expand_type(FLERR, "C1-N2-C1-N2", Atom::IMPROPER, lmp);
EXPECT_THAT(expanded, StrEq("1"));
delete[] expanded;
TEST_FAILURE(".*ERROR: Type string XX not found in labelmap.*",
utils::expand_type(FLERR, "XX", Atom::BOND, lmp););
}
} // namespace LAMMPS_NS

11
unittest/commands/test_variables.cpp
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@ -33,10 +33,10 @@
bool verbose = false;
namespace LAMMPS_NS {
using MathConst::MY_PI;
using ::testing::ContainsRegex;
using ::testing::ExitedWithCode;
using ::testing::StrEq;
using MathConst::MY_PI;
class VariableTest : public LAMMPSTest {
protected:
@ -196,8 +196,10 @@ TEST_F(VariableTest, CreateDelete)
TEST_FAILURE(".*ERROR: Illegal variable command.*", command("variable"););
TEST_FAILURE(".*ERROR: Illegal variable index command.*", command("variable dummy index"););
TEST_FAILURE(".*ERROR: Illegal variable delete command: expected 2 arguments but found 3.*", command("variable dummy delete xxx"););
TEST_FAILURE(".*ERROR: Invalid variable loop argument: -1.*", command("variable dummy loop -1"););
TEST_FAILURE(".*ERROR: Illegal variable delete command: expected 2 arguments but found 3.*",
command("variable dummy delete xxx"););
TEST_FAILURE(".*ERROR: Invalid variable loop argument: -1.*",
command("variable dummy loop -1"););
TEST_FAILURE(".*ERROR: Illegal variable loop command.*", command("variable dummy loop 10 1"););
TEST_FAILURE(".*ERROR: Unknown variable keyword: xxx.*", command("variable dummy xxxx"););
TEST_FAILURE(".*ERROR: Cannot redefine variable as a different style.*",
@ -402,7 +404,8 @@ TEST_F(VariableTest, Functions)
command("print \"$(extract_setting()\""););
TEST_FAILURE(".*ERROR: Invalid extract_setting.. function syntax in variable formula.*",
command("print \"$(extract_setting(one,two))\""););
TEST_FAILURE(".*ERROR: Unknown setting nprocs for extract_setting.. function in variable formula.*",
TEST_FAILURE(
".*ERROR: Unknown setting nprocs for extract_setting.. function in variable formula.*",
command("print \"$(extract_setting(nprocs))\""););
}