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rename "set spin" to "set spin/atom" and "set spin/random" to "set spin/atom/random"

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this also adds unit tests and improves error checking and messages
This commit is contained in:
Axel Kohlmeyer
2022-08-28 18:57:19 -04:00
parent bb6ea422b7
commit 74bbbb9e17
3 changed files with 178 additions and 21 deletions
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18
doc/src/set.rst
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@ -15,7 +15,7 @@ Syntax
* one or more keyword/value pairs may be appended
* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset*
or *mol* or *x* or *y* or *z* or *vx* or *vy* or *vz* or *charge* or
*dipole* or *dipole/random* or *quat* or *spin* or *spin/random* or
*dipole* or *dipole/random* or *quat* or *spin/atom* or *spin/atom/random* or
*quat* or *quat/random* or *diameter* or *shape* or
*length* or *tri* or *theta* or *theta/random* or *angmom* or
*omega* or *mass* or *density* or *density/disc* or
@ -55,11 +55,11 @@ Syntax
*dipole/random* value = seed Dlen
seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
*spin* values = g x y z
*spin/atom* values = g x y z
g = magnitude of magnetic spin vector (in Bohr magneton's unit)
x,y,z = orientation of magnetic spin vector
any of x,y,z can be an atom-style variable (see below)
*spin/random* value = seed Dlen
*spin/atom/random* value = seed Dlen
seed = random # seed (positive integer) for magnetic spin orientations
Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit)
*quat* values = a b c theta
@ -277,14 +277,18 @@ the orientation of a particular atom is the same, regardless of how
many processors are being used. This keyword does not allow use of an
atom-style variable.
Keyword *spin* uses the specified g value to set the magnitude of the
.. versionchanged:: TBD
Keyword *spin/atom* uses the specified g value to set the magnitude of the
magnetic spin vectors, and the x,y,z values as components of a vector
to set as the orientation of the magnetic spin vectors of the selected
atoms.
atoms. This keyword was previously called *spin*.
Keyword *spin/random* randomizes the orientation of the magnetic spin
.. versionchanged:: TBD
Keyword *spin/atom/random* randomizes the orientation of the magnetic spin
vectors for the selected atoms and sets the magnitude of each to the
specified *Dlen* value.
specified *Dlen* value. This keyword was previously called *spin/random*.
Keyword *quat* uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms. The

56
src/set.cpp
View File

@ -46,9 +46,9 @@ enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT};
enum{TYPE,TYPE_FRACTION,TYPE_RATIO,TYPE_SUBSET,
MOLECULE,X,Y,Z,VX,VY,VZ,CHARGE,MASS,SHAPE,LENGTH,TRI,
DIPOLE,DIPOLE_RANDOM,SPIN,SPIN_RANDOM,QUAT,QUAT_RANDOM,
THETA,THETA_RANDOM,ANGMOM,OMEGA,
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
DIPOLE,DIPOLE_RANDOM,SPIN_ATOM,SPIN_RANDOM,SPIN_ELECTRON,RADIUS_ELECTRON,
QUAT,QUAT_RANDOM,THETA,THETA_RANDOM,ANGMOM,OMEGA,
DIAMETER,RADIUS_ATOM,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
SPH_E,SPH_CV,SPH_RHO,EDPD_TEMP,EDPD_CV,CC,SMD_MASS_DENSITY,
SMD_CONTACT_RADIUS,DPDTHETA,EPSILON,IVEC,DVEC,IARRAY,DARRAY};
@ -265,8 +265,10 @@ void Set::command(int narg, char **arg)
setrandom(DIPOLE_RANDOM);
iarg += 3;
} else if (strcmp(arg[iarg],"spin") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
} else if ((strcmp(arg[iarg],"spin") == 0) || (strcmp(arg[iarg],"spin/atom") == 0)) {
if ((strcmp(arg[iarg],"spin") == 0) && (comm->me == 0))
error->warning(FLERR, "Set attribute spin is deprecated. Please use spin/atom instead.");
if (iarg+5 > narg) utils::missing_cmd_args(FLERR, "set spin/atom", error);
if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1],1);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (utils::strmatch(arg[iarg+2],"^v_")) varparse(arg[iarg+2],2);
@ -275,24 +277,50 @@ void Set::command(int narg, char **arg)
else yvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (utils::strmatch(arg[iarg+4],"^v_")) varparse(arg[iarg+4],4);
else zvalue = utils::numeric(FLERR,arg[iarg+4],false,lmp);
if ((xvalue == 0.0) && (yvalue == 0.0) && (zvalue == 0.0))
error->all(FLERR,"At least one spin vector component must be non-zero");
if (!atom->sp_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(SPIN);
error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style());
if (dvalue <= 0.0)
error->all(FLERR,"Invalid spin magnitude {} in set {} command", dvalue, arg[iarg]);
set(SPIN_ATOM);
iarg += 5;
} else if (strcmp(arg[iarg],"spin/random") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal set command");
} else if ((strcmp(arg[iarg],"spin/random") == 0) ||
(strcmp(arg[iarg],"spin/atom/random") == 0)) {
if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "set spin/atom/random", error);
ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
dvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if ((strcmp(arg[iarg],"spin/random") == 0) && (comm->me == 0))
error->warning(FLERR, "Set attribute spin/random is deprecated. "
"Please use spin/atom/random instead.");
if (!atom->sp_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style());
if (ivalue <= 0)
error->all(FLERR,"Invalid random number seed in set command");
error->all(FLERR,"Invalid random number seed {} in set {} command", ivalue, arg[iarg]);
if (dvalue <= 0.0)
error->all(FLERR,"Invalid dipole length in set command");
error->all(FLERR,"Invalid spin magnitude {} in set {} command", dvalue, arg[iarg]);
setrandom(SPIN_RANDOM);
iarg += 3;
} else if (strcmp(arg[iarg],"radius/electron") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set radius/electron", error);
if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1],1);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->eradius_flag)
error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style());
set(RADIUS_ELECTRON);
iarg += 2;
} else if (strcmp(arg[iarg],"spin/electron") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set spin/electron", error);
if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1],1);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->spin_flag)
error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style());
set(SPIN_ELECTRON);
iarg += 2;
} else if (strcmp(arg[iarg],"quat") == 0) {
if (iarg+5 > narg) utils::missing_cmd_args(FLERR, "set quat", error);
if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1],1);
@ -714,7 +742,7 @@ void Set::selection(int n)
} else if (style == GROUP_SELECT) {
int igroup = group->find(id);
if (igroup == -1) error->all(FLERR,"Could not find set group ID");
if (igroup == -1) error->all(FLERR,"Could not find set group ID {}", id);
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
@ -947,7 +975,7 @@ void Set::set(int keyword)
// set magnetic moments
else if (keyword == SPIN) {
else if (keyword == SPIN_ATOM) {
double **sp = atom->sp;
double inorm = 1.0/sqrt(xvalue*xvalue+yvalue*yvalue+zvalue*zvalue);
sp[i][0] = inorm*xvalue;

125
unittest/commands/test_set_property.cpp
View File

@ -87,6 +87,11 @@ TEST_F(SetTest, NoBoxNoAtoms)
TEST_FAILURE(".*ERROR: Unknown set command style: xxx.*", command("set xxx 1 x 0.0"););
TEST_FAILURE(".*ERROR: Set keyword or custom property yyy does not exist.*",
command("set type 1 yyy 0.0"););
TEST_FAILURE(".*ERROR: Cannot set attribute spin/atom for atom style atomic.*",
command("set atom * spin/atom 1.0 1.0 0.0 0.0"););
TEST_FAILURE(".*ERROR: Cannot set attribute spin/atom/random for atom style atomic.*",
command("set atom * spin/atom/random 436273456 1.0"););
}
TEST_F(SetTest, StylesTypes)
@ -161,6 +166,126 @@ TEST_F(SetTest, StylesTypes)
for (int i = 0; i < 8; ++i)
sum += (atom->type[i] == 2) ? 1 : 0;
ASSERT_EQ(sum, 4);
TEST_FAILURE(".*ERROR: Numeric index 9 is out of bounds .1-8.*", command("set type 9 x 0.0"););
TEST_FAILURE(".*ERROR: Invalid range string: 3:10.*", command("set type 3:10 x 0.0"););
TEST_FAILURE(".*ERROR: Could not find set group ID nope.*", command("set group nope x 0.0"););
}
TEST_F(SetTest, PosVelCharge)
{
atomic_system("charge");
ASSERT_EQ(atom->natoms, 8);
BEGIN_HIDE_OUTPUT();
command("set group top charge 1.0");
command("set atom 5*8 charge -1.0");
END_HIDE_OUTPUT();
EXPECT_EQ(atom->q[0], 1);
EXPECT_EQ(atom->q[1], 1);
EXPECT_EQ(atom->q[2], 0);
EXPECT_EQ(atom->q[3], 0);
EXPECT_EQ(atom->q[4], -1);
EXPECT_EQ(atom->q[5], -1);
EXPECT_EQ(atom->q[6], -1);
EXPECT_EQ(atom->q[7], -1);
BEGIN_HIDE_OUTPUT();
command("variable xpos atom 0.5-x");
command("variable ypos atom y*0.5");
command("set atom * x v_xpos y v_ypos z 0.5");
command("set group all vx v_xpos vy v_ypos vz 0.5");
END_HIDE_OUTPUT();
EXPECT_EQ(atom->x[0][0], 0.375);
EXPECT_EQ(atom->x[0][1], 0.0625);
EXPECT_EQ(atom->x[0][2], 0.5);
EXPECT_EQ(atom->x[1][0], -0.625);
EXPECT_EQ(atom->x[1][1], 0.0625);
EXPECT_EQ(atom->x[1][2], 0.5);
EXPECT_EQ(atom->x[2][0], 0.375);
EXPECT_EQ(atom->x[2][1], 0.5625);
EXPECT_EQ(atom->x[2][2], 0.5);
EXPECT_EQ(atom->x[3][0], -0.625);
EXPECT_EQ(atom->x[3][1], 0.5625);
EXPECT_EQ(atom->x[3][2], 0.5);
EXPECT_EQ(atom->x[4][0], 0.375);
EXPECT_EQ(atom->x[4][1], 0.0625);
EXPECT_EQ(atom->x[4][2], 0.5);
EXPECT_EQ(atom->x[5][0], -0.625);
EXPECT_EQ(atom->x[5][1], 0.0625);
EXPECT_EQ(atom->x[5][2], 0.5);
EXPECT_EQ(atom->x[6][0], 0.375);
EXPECT_EQ(atom->x[6][1], 0.5625);
EXPECT_EQ(atom->x[6][2], 0.5);
EXPECT_EQ(atom->x[7][0], -0.625);
EXPECT_EQ(atom->x[7][1], 0.5625);
EXPECT_EQ(atom->x[7][2], 0.5);
EXPECT_EQ(atom->v[0][0], 0.125);
EXPECT_EQ(atom->v[0][1], 0.03125);
EXPECT_EQ(atom->v[0][2], 0.5);
EXPECT_EQ(atom->v[1][0], 1.125);
EXPECT_EQ(atom->v[1][1], 0.03125);
EXPECT_EQ(atom->v[1][2], 0.5);
EXPECT_EQ(atom->v[2][0], 0.125);
EXPECT_EQ(atom->v[2][1], 0.28125);
EXPECT_EQ(atom->v[2][2], 0.5);
EXPECT_EQ(atom->v[3][0], 1.125);
EXPECT_EQ(atom->v[3][1], 0.28125);
EXPECT_EQ(atom->v[3][2], 0.5);
EXPECT_EQ(atom->v[4][0], 0.125);
EXPECT_EQ(atom->v[4][1], 0.03125);
EXPECT_EQ(atom->v[4][2], 0.5);
EXPECT_EQ(atom->v[5][0], 1.125);
EXPECT_EQ(atom->v[5][1], 0.03125);
EXPECT_EQ(atom->v[5][2], 0.5);
EXPECT_EQ(atom->v[6][0], 0.125);
EXPECT_EQ(atom->v[6][1], 0.28125);
EXPECT_EQ(atom->v[6][2], 0.5);
EXPECT_EQ(atom->v[7][0], 1.125);
EXPECT_EQ(atom->v[7][1], 0.28125);
EXPECT_EQ(atom->v[7][2], 0.5);
}
TEST_F(SetTest, SpinPackage)
{
if (!Info::has_package("SPIN")) GTEST_SKIP();
atomic_system("spin");
ASSERT_EQ(atom->natoms, 8);
BEGIN_HIDE_OUTPUT();
command("set atom 1*2 spin/atom 0.5 0.1 0.5 -0.1");
command("set atom 8 spin/atom/random 23974 0.25");
END_HIDE_OUTPUT();
constexpr double vx = 0.1;
constexpr double vy = 0.5;
constexpr double vz = -0.1;
constexpr double norm = 1.0 / sqrt(vx * vx + vy * vy + vz * vz);
EXPECT_EQ(atom->sp[0][0], vx * norm);
EXPECT_EQ(atom->sp[0][1], vy * norm);
EXPECT_EQ(atom->sp[0][2], vz * norm);
EXPECT_EQ(atom->sp[0][3], 0.5);
EXPECT_EQ(atom->sp[1][0], vx * norm);
EXPECT_EQ(atom->sp[1][1], vy * norm);
EXPECT_EQ(atom->sp[1][2], vz * norm);
EXPECT_EQ(atom->sp[1][3], 0.5);
EXPECT_NE(atom->sp[7][0], 0.0);
EXPECT_NE(atom->sp[7][1], 0.0);
EXPECT_NE(atom->sp[7][2], 0.0);
EXPECT_EQ(atom->sp[7][3], 0.25);
for (int i = 2; i < 7; ++i)
for (int j = 0; j < 4; ++j)
EXPECT_EQ(atom->sp[i][j], 0);
TEST_FAILURE(".*ERROR: Invalid spin magnitude -0.1 in set spin/atom command.*",
command("set atom * spin/atom -0.1 1.0 0.0 0.0"););
TEST_FAILURE(".*ERROR: At least one spin vector component must be non-zero.*",
command("set atom * spin/atom 1.0 0.0 0.0 0.0"););
TEST_FAILURE(".*ERROR: Invalid spin magnitude -0.2 in set spin/atom/random command.*",
command("set atom * spin/atom/random 436273456 -0.2"););
TEST_FAILURE(".*ERROR: Invalid random number seed 0 in set spin/atom/random command.*",
command("set atom * spin/atom/random 0 1.0"););
}
} // namespace LAMMPS_NS