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Merge pull request #2342 from lammps/fix-property-array

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Enable fix property/atom to create custom arrays
This commit is contained in:
Axel Kohlmeyer
2021-08-19 17:33:55 -04:00
committed by GitHub
parent 537f0eed8e f7c8b0c88b
commit 3404920e98
44 changed files with 1981 additions and 1162 deletions
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51
unittest/formats/test_atom_styles.cpp
View File

@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "../testing/core.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "atom_vec_ellipsoid.h"
@ -24,7 +25,6 @@
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include "../testing/core.h"
#include <cmath>
#include <cstdio>
@ -48,7 +48,7 @@
using LAMMPS_NS::utils::split_words;
static void create_molecule_files(const std::string & h2o_filename, const std::string & co2_filename)
static void create_molecule_files(const std::string &h2o_filename, const std::string &co2_filename)
{
// create molecule files
const char h2o_file[] = "# Water molecule. SPC/E model.\n\n3 atoms\n2 bonds\n1 angles\n\n"
@ -95,11 +95,10 @@ using ::testing::Eq;
class AtomStyleTest : public LAMMPSTest {
protected:
static void SetUpTestSuite() {
create_molecule_files("h2o.mol", "co2.mol");
}
static void SetUpTestSuite() { create_molecule_files("h2o.mol", "co2.mol"); }
static void TearDownTestSuite() {
static void TearDownTestSuite()
{
remove("h2o.mol");
remove("co2.mol");
}
@ -237,8 +236,10 @@ struct AtomState {
bool has_dihedral = false;
bool has_improper = false;
bool has_iname = false;
bool has_dname = false;
bool has_ivname = false;
bool has_dvname = false;
bool has_ianame = false;
bool has_daname = false;
bool has_mass = false;
bool has_mass_setflag = false;
@ -444,8 +445,10 @@ void ASSERT_ATOM_STATE_EQ(Atom *atom, const AtomState &expected)
ASSERT_EQ(atom->nivector, expected.nivector);
ASSERT_EQ(atom->ndvector, expected.ndvector);
ASSERT_ARRAY_ALLOCATED(atom->iname, expected.has_iname);
ASSERT_ARRAY_ALLOCATED(atom->dname, expected.has_dname);
ASSERT_ARRAY_ALLOCATED(atom->ivname, expected.has_ivname);
ASSERT_ARRAY_ALLOCATED(atom->dvname, expected.has_dvname);
ASSERT_ARRAY_ALLOCATED(atom->ianame, expected.has_ianame);
ASSERT_ARRAY_ALLOCATED(atom->daname, expected.has_daname);
ASSERT_ARRAY_ALLOCATED(atom->mass, expected.has_mass);
ASSERT_ARRAY_ALLOCATED(atom->mass_setflag, expected.has_mass_setflag);
@ -4555,7 +4558,8 @@ TEST_F(AtomStyleTest, property_atom)
{
BEGIN_HIDE_OUTPUT();
command("atom_modify map array");
command("fix Properties all property/atom i_one d_two mol d_three q rmass ghost yes");
command("fix Properties all property/atom "
"i_one d_two mol d_three q rmass i2_four 2 d2_five 3 ghost yes");
END_HIDE_OUTPUT();
AtomState expected;
@ -4570,8 +4574,10 @@ TEST_F(AtomStyleTest, property_atom)
expected.has_x = true;
expected.has_v = true;
expected.has_f = true;
expected.has_iname = true;
expected.has_dname = true;
expected.has_ivname = true;
expected.has_dvname = true;
expected.has_ianame = true;
expected.has_daname = true;
expected.has_extra_grow = true;
expected.has_extra_restart = true;
expected.has_extra_border = true;
@ -4614,7 +4620,12 @@ TEST_F(AtomStyleTest, property_atom)
command("set atom 2 d_three -1.0");
command("set atom 3 d_three 0.5");
command("set atom 4 d_three 2.0");
command("set atom * d2_five[1] -5.9");
command("set atom * d2_five[2] 1.1e-2");
command("set atom * d2_five[3] .1");
command("set atom 1*2 i2_four[1] -2");
command("set atom 3*4 i2_four[1] -1");
command("set atom * i2_four[2] 2");
END_HIDE_OUTPUT();
expected.natoms = 4;
expected.nlocal = 4;
@ -4637,7 +4648,8 @@ TEST_F(AtomStyleTest, property_atom)
command("pair_style zero 4.0");
command("units real");
command("atom_modify map array");
command("fix props all property/atom i_one d_two mol d_three q rmass ghost yes");
command("fix props all property/atom i_one d_two mol d_three q rmass "
"i2_four 2 d2_five 3 ghost yes");
command("read_data test_atom_styles.data fix props NULL Properties");
command("pair_coeff * *");
END_HIDE_OUTPUT();
@ -4726,7 +4738,8 @@ TEST_F(AtomStyleTest, property_atom)
command("clear");
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
command("read_restart test_atom_styles.restart");
command("fix props all property/atom i_one d_two mol d_three q rmass ghost yes");
command("fix props all property/atom i_one d_two mol d_three q rmass "
"i2_four 2 d2_five 3 ghost yes");
END_HIDE_OUTPUT();
expected.natoms = 2;
expected.nlocal = 2;
@ -4738,7 +4751,11 @@ TEST_F(AtomStyleTest, property_atom)
expected.has_mass_setflag = true;
expected.has_sametag = true;
expected.has_extra = true;
expected.nextra_store = 7;
expected.has_ivname = true;
expected.has_dvname = true;
expected.has_ianame = true;
expected.has_daname = true;
expected.nextra_store = 12;
ASSERT_ATOM_STATE_EQ(lmp->atom, expected);
ASSERT_NE(lmp->atom->avec, nullptr);

11
unittest/utils/test_utils.cpp
View File

@ -478,6 +478,17 @@ TEST(Utils, strmatch_opt_char)
{
ASSERT_TRUE(utils::strmatch("rigid", "^r?igid"));
ASSERT_TRUE(utils::strmatch("igid", "^r?igid"));
ASSERT_TRUE(utils::strmatch("c_name","^[cfvid]2?_name"));
ASSERT_TRUE(utils::strmatch("f_name","^[cfvid]2?_name"));
ASSERT_TRUE(utils::strmatch("v_name","^[cfvid]2?_name"));
ASSERT_TRUE(utils::strmatch("i_name","^[cfvid]2?_name"));
ASSERT_TRUE(utils::strmatch("d_name","^[cfvid]2?_name"));
ASSERT_TRUE(utils::strmatch("i2_name","^[cfvid]2?_name"));
ASSERT_TRUE(utils::strmatch("d2_name","^[cfvid]2?_name"));
ASSERT_FALSE(utils::strmatch("d2name","^[cfvid]2?_name"));
ASSERT_FALSE(utils::strmatch("i1_name","^[cfvid]2?_name"));
ASSERT_FALSE(utils::strmatch("V_name","^[cfvid]2?_name"));
ASSERT_FALSE(utils::strmatch("x_name","^[cfvid]2?_name"));
}
TEST(Utils, strmatch_dot)