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enforce atom z coords = 0.0 for 2d simulations

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This commit is contained in:
Steve Plimpton
2023-09-06 09:04:10 -06:00
parent 6f01b27e7e
commit d6d65f001a
5 changed files with 64 additions and 13 deletions
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13
src/atom.cpp
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@ -49,6 +49,7 @@ using namespace MathConst;
#define DELTA 1
#define EPSILON 1.0e-6
#define EPS_ZCOORD 1.0e-12
#define MAXLINE 256
/* ----------------------------------------------------------------------
@ -1076,6 +1077,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// ensures all data atoms will be owned even with round-off
int dimension = domain->dimension;
int triclinic = domain->triclinic;
double epsilon[3];
@ -1165,7 +1167,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
imx = utils::inumeric(FLERR,values[iptr],false,lmp);
imy = utils::inumeric(FLERR,values[iptr+1],false,lmp);
imz = utils::inumeric(FLERR,values[iptr+2],false,lmp);
if ((domain->dimension == 2) && (imz != 0))
if ((dimension == 2) && (imz != 0))
error->all(FLERR,"Z-direction image flag must be 0 for 2d-systems");
if ((!domain->xperiodic) && (imx != 0)) { reset_image_flag[0] = true; imx = 0; }
if ((!domain->yperiodic) && (imy != 0)) { reset_image_flag[1] = true; imy = 0; }
@ -1179,6 +1181,15 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
xdata[1] = utils::numeric(FLERR,values[xptr+1],false,lmp);
xdata[2] = utils::numeric(FLERR,values[xptr+2],false,lmp);
// for 2d simulation, check if z coord is within EPS_ZCOORD of zero
// then set to zero
if (dimension == 2) {
if (fabs(xdata[2]) > EPS_ZCOORD)
error->all(FLERR,"Read_data atom z coord is non-zero for 2d simulation");
xdata[2] = 0.0;
}
// convert atom coords from general triclinic to restricted triclinic
if (triclinic_general) domain->general_to_restricted_coords(xdata);

17
src/create_atoms.cpp
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@ -54,6 +54,8 @@ static constexpr double INV_P_CONST = 0.7548777;
static constexpr double INV_SQ_P_CONST = 0.5698403;
static constexpr int DEFAULT_MAXTRY = 1000;
#define EPS_ZCOORD 1.0e-12
enum { BOX, REGION, SINGLE, RANDOM, MESH };
enum { ATOM, MOLECULE };
enum { COUNT, INSERT, INSERT_SELECTED };
@ -1272,6 +1274,7 @@ void CreateAtoms::add_lattice()
// decrement lo, increment hi to avoid round-off issues in lattice->bbox(),
// which can lead to missing atoms in rare cases
// extra decrement of lo if min < 0, since static_cast(-1.5) = -1
// for 2d simulation, klo = khi = 0 so just one plane of atoms
ilo = static_cast<int>(xmin) - 1;
jlo = static_cast<int>(ymin) - 1;
@ -1284,7 +1287,7 @@ void CreateAtoms::add_lattice()
if (ymin < 0.0) jlo--;
if (zmin < 0.0) klo--;
printf("LOOP LATTICE bounds: %d %d: %d %d: %d %d\n",ilo,ihi,jlo,jhi,klo,khi);
if (domain->dimension == 2) klo = khi = 0;
// count lattice sites on each proc
@ -1351,6 +1354,7 @@ void CreateAtoms::loop_lattice(int action)
{
int i, j, k, m;
int dimension = domain->dimension;
int triclinic_general = domain->triclinic_general;
const double *const *const basis = domain->lattice->basis;
@ -1372,8 +1376,17 @@ void CreateAtoms::loop_lattice(int action)
domain->lattice->lattice2box(x[0], x[1], x[2]);
// convert from general to restricted triclinic coords
// for 2d simulation, check if z coord is within EPS_ZCOORD of zero
// then set to zero
if (triclinic_general) domain->general_to_restricted_coords(x);
if (triclinic_general) {
domain->general_to_restricted_coords(x);
if (dimension == 2) {
if (fabs(x[2]) > EPS_ZCOORD)
error->all(FLERR,"Create_atoms atom z coord is non-zero for 2d simulation");
x[2] = 0.0;
}
}
// if a region was specified, test if atom is in it

11
src/create_box.cpp
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@ -63,6 +63,7 @@ void CreateBox::command(int narg, char **arg)
int iarg = 2;
if (region) {
// region is not prism
// setup orthogonal box
// set simulation domain from region extent
@ -94,6 +95,11 @@ void CreateBox::command(int narg, char **arg)
domain->yz = prism->yz;
}
if (domain->dimension == 2) {
if (domain->boxlo[2] >= 0.0 || domain->boxhi[2] <= 0.0)
error->all(FLERR,"Create_box region zlo/zhi for 2d simulation must straddle 0.0");
}
// setup general triclinic box (with no region)
// read next box extent arguments to create ABC edge vectors + origin
// define_general_triclinic() converts
@ -115,6 +121,11 @@ void CreateBox::command(int narg, char **arg)
double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp);
iarg += 6;
if (domain->dimension == 2) {
if (clo >= 0.0 || clo <= 0.0)
error->all(FLERR,"Create_box region clo/chi for 2d simulation must straddle 0.0");
}
// use lattice2box() to generate origin and ABC vectors
// origin = abc lo
// ABC vectors = hi in one dim - origin

6
src/lattice.cpp
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@ -238,14 +238,14 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (dimension == 2) {
if (origin[2] != 0.0)
error->all(FLERR,
"Lattice settings are not compatible with 2d simulation");
"Lattice origin not compatible with 2d simulation");
if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0)
error->all(FLERR,
"Lattice settings are not compatible with 2d simulation");
"Lattice a1/a2/a3 vectors are not compatible with 2d simulation");
if (orientx[2] != 0 || orienty[2] != 0 ||
orientz[0] != 0 || orientz[1] != 0)
error->all(FLERR,
"Lattice settings are not compatible with 2d simulation");
"Lattice orient vectors are not compatible with 2d simulation");
}
if (spaceflag) {

22
src/read_data.cpp
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@ -491,11 +491,14 @@ void ReadData::command(int narg, char **arg)
boxlo[0] = boxlo[1] = boxlo[2] = -0.5;
boxhi[0] = boxhi[1] = boxhi[2] = 0.5;
avec[0] = avec[1] = avec[2] = 0.0;
bvec[0] = bvec[1] = bvec[2] = 0.0;
cvec[0] = cvec[1] = cvec[2] = 0.0;
xy = xz = yz = 0.0;
avec[0] = bvec[1] = cvec[2] = 1.0;
avec[1] = avec[2] = 0.0;
bvec[0] = bvec[2] = 0.0;
cvec[0] = cvec[1] = 0.0;
abc_origin[0] = abc_origin[1] = abc_origin[2] = 0.0;
if (domain->dimension == 2) abc_origin[2] = -0.5;
keyword[0] = '\0';
@ -527,6 +530,19 @@ void ReadData::command(int narg, char **arg)
triclinic = triclinic_general = 1;
}
// check if simulation box specified correctly for 2d
if (domain->dimension == 2) {
if (triclinic_general == 0) {
if (boxlo[2] >= 0.0 || boxhi[2] <= 0.0)
error->all(FLERR,"Read_data zlo/zhi for 2d simulation must straddle 0.0");
} else if (triclinic_general == 1) {
if (cvec[0] != 0.0 || cvec[1] != 0.0 || cvec[2] != 1.0 || abc_origin[2] != -0.5)
error->all(FLERR,"Read_data cvec and/or abc_origin is invalid for "
"2d simulation with general triclinic box");
}
}
// problem setup using info from header
// only done once, if firstpass and first data file
// apply extra settings before grow(), even if no topology in file