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Merge pull request #4046 from akohlmey/molecule-dipole

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Add support for Dipoles section to molecule files
This commit is contained in:
Axel Kohlmeyer
2024-01-18 14:57:01 -05:00
committed by GitHub
parent 14abc184f8 f23ba8fbad
commit fe1b568241
5 changed files with 268 additions and 57 deletions
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138
doc/src/molecule.rst
View File

@ -126,14 +126,50 @@ molecule (header keyword = inertia).
Format of a molecule file
"""""""""""""""""""""""""
The format of an individual molecule file is similar but
(not identical) to the data file read by the :doc:`read_data <read_data>`
commands, and is as follows.
The format of an individual molecule file looks similar but is
different than that of a data file read by the :doc:`read_data <read_data>`
commands. Here is a simple example for a TIP3P water molecule:
.. code-block::
# Water molecule. TIP3P geometry
# header section:
3 atoms
2 bonds
1 angles
# body section:
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
Types
1 1 # O
2 2 # H
3 2 # H
Charges
1 -0.834
2 0.417
3 0.417
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
A molecule file has a header and a body. The header appears first. The
first line of the header and thus of the molecule file is *always* skipped;
it typically contains a description of the file or a comment from the software
that created the file.
first line of the header and thus of the molecule file is *always*
skipped; it typically contains a description of the file or a comment
from the software that created the file.
Then lines are read one line at a time. Lines can have a trailing
comment starting with '#' that is ignored. There *must* be at least one
@ -158,25 +194,62 @@ appear if the value(s) are different than the default, except when
defining a *body* particle, which requires setting the number of
*atoms* to 1, and setting the *inertia* in a specific section (see below).
* N *atoms* = # of atoms N in molecule, default = 0
* Nb *bonds* = # of bonds Nb in molecule, default = 0
* Na *angles* = # of angles Na in molecule, default = 0
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
* Ni *impropers* = # of impropers Ni in molecule, default = 0
* Nf *fragments* = # of fragments Nf in molecule, default = 0
* Ninteger Ndouble *body* = # of integer and floating-point values
in body particle, default = 0
* Mtotal *mass* = total mass of molecule
* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
.. list-table::
:header-rows: 1
:widths: auto
For *mass*, *com*, and *inertia*, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consist of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
pre-compute them yourself and list the values in the file.
* - Number(s)
- Keyword
- Meaning
- Default Value
* - N
- atoms
- # of atoms N in molecule
- 0
* - Nb
- bonds
- # of bonds Nb in molecule
- 0
* - Na
- angles
- # of angles Na in molecule
- 0
* - Nd
- dihedrals
- # of dihedrals Nd in molecule
- 0
* - Ni
- impropers
- # of impropers Ni in molecule
- 0
* - Nf
- fragments
- # of fragments Nf in molecule
- 0
* - Ninteger Ndouble
- body
- # of integer and floating-point values in body particle
- 0
* - Mtotal
- mass
- total mass of molecule
- computed
* - Xc Yc Zc
- com
- coordinates of center-of-mass of molecule
- computed
* - Ixx Iyy Izz Ixy Ixz Iyz
- inertia
- 6 components of inertia tensor of molecule
- computed
For *mass*, *com*, and *inertia*, the default is for LAMMPS to calculate
this quantity itself if needed, assuming the molecules consist of a set
of point particles or finite-size particles (with a non-zero diameter)
that do **not** overlap. If finite-size particles in the molecule
**do** overlap, LAMMPS will not account for the overlap effects when
calculating any of these 3 quantities, so you should pre-compute them
yourself and list the values in the file.
The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
@ -188,7 +261,7 @@ internally.
These are the allowed section keywords for the body of the file.
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Dipoles, Masses* = atom-property sections
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@ -303,6 +376,21 @@ not listed, the default diameter of each atom in the molecule is 1.0.
----------
..versionadded:: TBD
*Dipoles* section:
* one line per atom
* line syntax: ID mux muy muz
* mux,muy,muz = x-, y-, and z-component of point dipole vector of atom
This section is only allowed for :doc:`atom styles <atom_style>` that
support particles with point dipoles, e.g. atom_style dipole. If not
listed, the default dipole component of each atom in the molecule is set
to 0.0.
----------
*Masses* section:
* one line per atom

10
src/atom.cpp
View File

@ -26,6 +26,7 @@
#include "input.h"
#include "label_map.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "molecule.h"
@ -2112,6 +2113,15 @@ std::vector<Molecule *>Atom::get_molecule_by_id(const std::string &id)
void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint offset)
{
if (onemol->qflag && q_flag) q[ilocal] = onemol->q[iatom];
if (onemol->muflag && mu_flag) {
double r[3], rotmat[3][3];
MathExtra::quat_to_mat(onemol->quat_external, rotmat);
MathExtra::matvec(rotmat, onemol->mu[iatom], r);
mu[ilocal][0] = r[0];
mu[ilocal][1] = r[1];
mu[ilocal][2] = r[2];
mu[ilocal][3] = sqrt(r[0] * r[0] + r[1] * r[1] + r[2] * r[2]);
}
if (onemol->radiusflag && radius_flag) radius[ilocal] = onemol->radius[iatom];
if (onemol->rmassflag && rmass_flag) rmass[ilocal] = onemol->rmass[iatom];
else if (rmass_flag)

85
src/molecule.cpp
View File

@ -41,15 +41,16 @@ using namespace LAMMPS_NS;
Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
Pointers(lmp), id(nullptr), x(nullptr), type(nullptr), molecule(nullptr), q(nullptr),
radius(nullptr), rmass(nullptr), num_bond(nullptr), bond_type(nullptr), bond_atom(nullptr),
num_angle(nullptr), angle_type(nullptr), angle_atom1(nullptr), angle_atom2(nullptr),
angle_atom3(nullptr), num_dihedral(nullptr), dihedral_type(nullptr), dihedral_atom1(nullptr),
dihedral_atom2(nullptr), dihedral_atom3(nullptr), dihedral_atom4(nullptr),
num_improper(nullptr), improper_type(nullptr), improper_atom1(nullptr), improper_atom2(nullptr),
improper_atom3(nullptr), improper_atom4(nullptr), nspecial(nullptr), special(nullptr),
shake_flag(nullptr), shake_atom(nullptr), shake_type(nullptr), avec_body(nullptr),
ibodyparams(nullptr), dbodyparams(nullptr), fragmentmask(nullptr), dx(nullptr), dxcom(nullptr),
dxbody(nullptr), quat_external(nullptr), fp(nullptr), count(nullptr)
radius(nullptr), rmass(nullptr), mu(nullptr), num_bond(nullptr), bond_type(nullptr),
bond_atom(nullptr), num_angle(nullptr), angle_type(nullptr), angle_atom1(nullptr),
angle_atom2(nullptr), angle_atom3(nullptr), num_dihedral(nullptr), dihedral_type(nullptr),
dihedral_atom1(nullptr), dihedral_atom2(nullptr), dihedral_atom3(nullptr),
dihedral_atom4(nullptr), num_improper(nullptr), improper_type(nullptr), improper_atom1(nullptr),
improper_atom2(nullptr), improper_atom3(nullptr), improper_atom4(nullptr), nspecial(nullptr),
special(nullptr), shake_flag(nullptr), shake_atom(nullptr), shake_type(nullptr),
avec_body(nullptr), ibodyparams(nullptr), dbodyparams(nullptr), fragmentmask(nullptr),
dx(nullptr), dxcom(nullptr), dxbody(nullptr), quat_external(nullptr), fp(nullptr),
count(nullptr)
{
me = comm->me;
@ -132,7 +133,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
// initialize all fields to empty
initialize();
Molecule::initialize();
// scan file for sizes of all fields and allocate storage for them
@ -141,28 +142,30 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
if (fp == nullptr)
error->one(FLERR, "Cannot open molecule file {}: {}", arg[ifile], utils::getsyserror());
}
read(0);
Molecule::read(0);
if (me == 0) fclose(fp);
allocate();
Molecule::allocate();
// read file again to populate all fields
if (me == 0) fp = fopen(arg[ifile], "r");
read(1);
Molecule::read(1);
if (me == 0) fclose(fp);
// stats
if (title.empty()) title = "(no title)";
if (me == 0)
utils::logmesg(lmp,
"Read molecule template {}:\n {} molecules\n"
"Read molecule template {}:\n{}\n"
" {} molecules\n"
" {} fragments\n"
" {} atoms with max type {}\n"
" {} bonds with max type {}\n"
" {} angles with max type {}\n"
" {} dihedrals with max type {}\n"
" {} impropers with max type {}\n",
id, nmolecules, nfragments, natoms, ntypes, nbonds, nbondtypes, nangles,
id, title, nmolecules, nfragments, natoms, ntypes, nbonds, nbondtypes, nangles,
nangletypes, ndihedrals, ndihedraltypes, nimpropers, nimpropertypes);
}
@ -423,6 +426,8 @@ void Molecule::read(int flag)
if (eof == nullptr) error->one(FLERR, "Unexpected end of molecule file");
}
if (flag == 0) title = utils::trim(line);
// read header lines
// skip blank lines or lines that start with "#"
// stop when read an unrecognized line
@ -572,6 +577,12 @@ void Molecule::read(int flag)
diameters(line);
else
skip_lines(natoms, line, keyword);
} else if (keyword == "Dipoles") {
muflag = 1;
if (flag)
dipoles(line);
else
skip_lines(natoms, line, keyword);
} else if (keyword == "Masses") {
rmassflag = 1;
if (flag)
@ -948,6 +959,40 @@ void Molecule::diameters(char *line)
}
}
/* ----------------------------------------------------------------------
read charges from file
------------------------------------------------------------------------- */
void Molecule::dipoles(char *line)
{
for (int i = 0; i < natoms; i++) count[i] = 0;
try {
for (int i = 0; i < natoms; i++) {
readline(line);
ValueTokenizer values(utils::trim_comment(line));
if ((int) values.count() != 4)
error->all(FLERR, "Invalid line in Dipoles section of molecule file: {}", line);
int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms)
error->all(FLERR, "Invalid atom index in Dipoles section of molecule file");
count[iatom]++;
mu[iatom][0] = values.next_double();
mu[iatom][1] = values.next_double();
mu[iatom][2] = values.next_double();
}
} catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Dipoles section of molecule file: {}\n{}", e.what(), line);
}
for (int i = 0; i < natoms; i++) {
if (count[i] == 0)
error->all(FLERR, "Atom {} missing in Dipoles section of molecule file", i + 1);
}
}
/* ----------------------------------------------------------------------
read masses from file
------------------------------------------------------------------------- */
@ -1828,6 +1873,7 @@ void Molecule::check_attributes()
int mismatch = 0;
if (qflag && !atom->q_flag) mismatch = 1;
if (muflag && !atom->mu_flag) mismatch = 1;
if (radiusflag && !atom->radius_flag) mismatch = 1;
if (rmassflag && !atom->rmass_flag) mismatch = 1;
@ -1869,6 +1915,7 @@ void Molecule::check_attributes()
void Molecule::initialize()
{
title.clear();
natoms = 0;
nbonds = nangles = ndihedrals = nimpropers = 0;
ntypes = 0;
@ -1880,7 +1927,7 @@ void Molecule::initialize()
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
maxspecial = 0;
xflag = typeflag = moleculeflag = fragmentflag = qflag = radiusflag = rmassflag = 0;
xflag = typeflag = moleculeflag = fragmentflag = qflag = radiusflag = muflag = rmassflag = 0;
bondflag = angleflag = dihedralflag = improperflag = 0;
nspecialflag = specialflag = 0;
shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
@ -1943,6 +1990,7 @@ void Molecule::allocate()
for (int j = 0; j < natoms; j++) fragmentmask[i][j] = 0;
}
if (qflag) memory->create(q, natoms, "molecule:q");
if (muflag) memory->create(mu, natoms, 3, "molecule:mu");
if (radiusflag) memory->create(radius, natoms, "molecule:radius");
if (rmassflag) memory->create(rmass, natoms, "molecule:rmass");
@ -2167,6 +2215,11 @@ void Molecule::print()
for (int i = 0; i < natoms; i++)
printf(" %d %g\n",i+1,radius[i]);
}
if (muflag) {
printf( "Dipoles:\n");
for (int i = 0; i < natoms; i++)
printf(" %d %g %g %g\n",i+1,mu[i][0],mu[i][1],mu[i][2]);
}
if (rmassflag) {
printf( "Masses:\n");
for (int i = 0; i < natoms; i++)

6
src/molecule.h
View File

@ -25,6 +25,8 @@ class Molecule : protected Pointers {
// else 0 if not first in set
int last; // 1 if last molecule in set, else 0
std::string title; // title string of the molecule file
// number of atoms,bonds,etc in molecule
// nibody,ndbody = # of integer/double fields in body
@ -41,7 +43,7 @@ class Molecule : protected Pointers {
// 1 if attribute defined in file, 0 if not
int xflag, typeflag, moleculeflag, fragmentflag, qflag, radiusflag, rmassflag;
int xflag, typeflag, moleculeflag, fragmentflag, qflag, radiusflag, muflag, rmassflag;
int bondflag, angleflag, dihedralflag, improperflag;
int nspecialflag, specialflag;
int shakeflag, shakeflagflag, shakeatomflag, shaketypeflag;
@ -63,6 +65,7 @@ class Molecule : protected Pointers {
double *q; // charge on each atom
double *radius; // radius of each atom
double *rmass; // mass of each atom
double **mu; // dipole vector of each atom
int *num_bond; // bonds, angles, dihedrals, impropers for each atom
int **bond_type;
@ -142,6 +145,7 @@ class Molecule : protected Pointers {
void fragments(char *);
void charges(char *);
void diameters(char *);
void dipoles(char *);
void masses(char *);
void bonds(int, char *);
void angles(int, char *);

86
unittest/formats/test_molecule_file.cpp
View File

@ -32,6 +32,8 @@ using testing::StrEq;
using utils::split_words;
const double EPSILON = 5.0e-14;
#define test_name test_info_->name()
static void create_molecule_files(const std::string &h2o_filename, const std::string &co2_filename)
@ -145,7 +147,7 @@ protected:
fclose(fp);
command(fmt::format("molecule {} {} {}", name, file, args));
remove(file.c_str());
platform::unlink(file.c_str());
}
};
@ -184,7 +186,7 @@ TEST_F(MoleculeFileTest, badargs)
TEST_FAILURE(
".*Illegal molecule command.*",
run_mol_cmd(test_name, "scale", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
remove("badargs.mol");
platform::unlink("moltest_badargs.mol");
}
TEST_F(MoleculeFileTest, noatom)
@ -193,14 +195,14 @@ TEST_F(MoleculeFileTest, noatom)
run_mol_cmd(test_name, "",
"Comment\n0 atoms\n1 bonds\n\n"
" Coords\n\nBonds\n\n 1 1 2\n"););
remove("noatom.mol");
platform::unlink("moltest_noatom.mol");
}
TEST_F(MoleculeFileTest, empty)
{
TEST_FAILURE(".*ERROR: Unexpected end of molecule file.*",
run_mol_cmd(test_name, "", "Comment\n\n"););
remove("empty.mol");
platform::unlink("moltest_empty.mol");
}
TEST_F(MoleculeFileTest, nospecial)
@ -210,7 +212,7 @@ TEST_F(MoleculeFileTest, nospecial)
"Comment\n3 atoms\n\n2 bonds\n\n"
" Coords\n\n 1 1.0 1.0 1.0\n 2 1.0 1.0 0.0\n 3 1.0 0.0 1.0\n"
" Bonds\n\n 1 1 1 2\n 2 1 1 3\n"););
remove("nospecial.mol");
platform::unlink("moltest_nospecial.mol");
}
TEST_F(MoleculeFileTest, minimal)
@ -218,7 +220,7 @@ TEST_F(MoleculeFileTest, minimal)
BEGIN_CAPTURE_OUTPUT();
run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*1 molecules.*\n"
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Comment.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*1 atoms.*\n.*0 bonds.*"));
}
@ -230,7 +232,7 @@ TEST_F(MoleculeFileTest, notype)
command("create_box 1 box");
run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*1 molecules.*\n"
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Comment.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*1 atoms.*\n.*0 bonds.*"));
TEST_FAILURE(".*ERROR: Create_atoms molecule must have atom types.*",
command("create_atoms 0 single 0.0 0.0 0.0 mol notype 542465"););
@ -259,7 +261,7 @@ TEST_F(MoleculeFileTest, twomols)
" Coords\n\n 1 0.0 0.0 0.0\n 2 0.0 0.0 1.0\n"
" Molecules\n\n 1 1\n 2 2\n\n Types\n\n 1 1\n 2 2\n\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*2 molecules.*\n"
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Comment.*\n.*2 molecules.*\n"
".*0 fragments.*\n.*2 atoms with max type 2.*\n.*0 bonds.*"));
ASSERT_EQ(lmp->atom->nmolecule, 1);
auto mols = lmp->atom->get_molecule_by_id(test_name);
@ -273,10 +275,10 @@ TEST_F(MoleculeFileTest, twofiles)
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(
output,
ContainsRegex(".*Read molecule template twomols:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template twomols:.*\n.*Water.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 2.*\n.*2 bonds with max type 1.*\n"
".*1 angles with max type 1.*\n.*0 dihedrals.*\n.*0 impropers.*\n"
".*Read molecule template twomols:.*\n.*1 molecules.*\n"
".*Read molecule template twomols:.*\n.*CO2.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
".*1 angles with max type 2.*\n.*0 dihedrals.*"));
BEGIN_CAPTURE_OUTPUT();
@ -306,7 +308,7 @@ TEST_F(MoleculeFileTest, labelmap)
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(
output,
ContainsRegex(".*Read molecule template h2olabel:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template h2olabel:.*\n.*Water.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 2.*\n.*2 bonds with max type 1.*\n"
".*1 angles with max type 1.*\n.*0 dihedrals.*\n.*0 impropers.*"));
BEGIN_CAPTURE_OUTPUT();
@ -314,7 +316,7 @@ TEST_F(MoleculeFileTest, labelmap)
output = END_CAPTURE_OUTPUT();
ASSERT_THAT(
output,
ContainsRegex(".*Read molecule template co2label:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template co2label:.*\n.*CO2.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
".*1 angles with max type 2.*\n.*0 dihedrals.*"));
BEGIN_CAPTURE_OUTPUT();
@ -328,12 +330,12 @@ TEST_F(MoleculeFileTest, labelmap)
auto second = output.substr(mark);
ASSERT_THAT(
first,
ContainsRegex(".*Read molecule template h2onum:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template h2onum:.*\n.*Water.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 2.*\n.*2 bonds with max type 1.*\n"
".*1 angles with max type 1.*\n.*0 dihedrals.*\n.*0 impropers.*\n"));
ASSERT_THAT(
second,
ContainsRegex(".*Read molecule template co2num:.*\n.*1 molecules.*\n"
ContainsRegex(".*Read molecule template co2num:.*\n.*CO2.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
".*1 angles with max type 2.*\n.*0 dihedrals.*"));
ASSERT_EQ(lmp->atom->nmolecule, 4);
@ -379,7 +381,7 @@ TEST_F(MoleculeFileTest, bonds)
" 1 1 1 2\n"
" 2 2 1 3\n\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*1 molecules.*\n"
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Comment.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*4 atoms.*type.*2.*\n"
".*2 bonds.*type.*2.*\n.*0 angles.*"));
@ -404,6 +406,60 @@ TEST_F(MoleculeFileTest, bonds)
END_HIDE_OUTPUT();
}
TEST_F(MoleculeFileTest, dipoles)
{
if (!LAMMPS::is_installed_pkg("DIPOLE")) GTEST_SKIP();
BEGIN_CAPTURE_OUTPUT();
command("atom_style dipole");
command("region box block 0 1 0 1 0 1");
command("create_box 2 box");
run_mol_cmd(test_name, "",
"# Dumbbell with dipole molecule file.\n\n"
"2 atoms\n\n"
"Coords\n\n1 -1.0 0.0 0.0\n2 1.0 0.0 0.0\n\n"
"Types\n\n1 1\n2 2\n\n"
"Dipoles\n\n1 1.0 0.0 0.0\n2 1.0 1.0 0.0\n\n");
auto output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*Dumbbell.*\n.*1 molecules.*\n"
".*0 fragments.*\n.*2 atoms.*type.*2.*\n"));
BEGIN_CAPTURE_OUTPUT();
command("mass * 1.0");
command("create_atoms 0 single 0.5 0.5 0.5 mol dipoles 67235 rotate 90.0 0.0 0.0 1.0");
output = END_CAPTURE_OUTPUT();
ASSERT_THAT(output, ContainsRegex(".*Created 2 atoms.*"));
Molecule *mol = lmp->atom->molecules[0];
ASSERT_EQ(mol->natoms, 2);
ASSERT_EQ(lmp->atom->natoms, 2);
mol->compute_mass();
mol->compute_com();
EXPECT_NEAR(mol->masstotal, 2.0, EPSILON);
EXPECT_NEAR(mol->com[0], 0.0, EPSILON);
EXPECT_NEAR(mol->com[1], 0.0, EPSILON);
EXPECT_NEAR(mol->com[2], 0.0, EPSILON);
EXPECT_EQ(mol->comatom, 1);
ASSERT_NE(mol->mu, nullptr);
EXPECT_NEAR(mol->mu[0][0], 1.0, EPSILON);
EXPECT_NEAR(mol->mu[0][1], 0.0, EPSILON);
EXPECT_NEAR(mol->mu[0][2], 0.0, EPSILON);
EXPECT_NEAR(mol->mu[1][0], 1.0, EPSILON);
EXPECT_NEAR(mol->mu[1][1], 1.0, EPSILON);
EXPECT_NEAR(mol->mu[1][2], 0.0, EPSILON);
EXPECT_NEAR(mol->maxextent, 2.0, EPSILON);
// dipoles should be rotated by 90 degrees clockwise around the z axis
double **mu = lmp->atom->mu;
ASSERT_NE(mu, nullptr);
EXPECT_NEAR(mu[0][0], 0.0, EPSILON);
EXPECT_NEAR(mu[0][1], 1.0, EPSILON);
EXPECT_NEAR(mu[0][2], 0.0, EPSILON);
EXPECT_NEAR(mu[0][3], 1.0, EPSILON);
EXPECT_NEAR(mu[1][0], -1.0, EPSILON);
EXPECT_NEAR(mu[1][1], 1.0, EPSILON);
EXPECT_NEAR(mu[1][2], 0.0, EPSILON);
EXPECT_NEAR(mu[1][3], sqrt(2.0), EPSILON);
}
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);