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fix homepage urls, tabs & trailing whitespace, remove errors from headers

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This commit is contained in:
Axel Kohlmeyer
2022-06-17 12:48:24 -04:00
parent e201d6e77e
commit f27e9941ae
10 changed files with 175 additions and 225 deletions
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4
doc/src/compute.rst
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@ -284,8 +284,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
* :doc:`snap <compute_sna_atom>` - gradients of SNAP energy and forces w.r.t. linear coefficients and related quantities for fitting SNAP potentials
* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
* :doc:`sna/grid <compute_sna_atom>` - global array of bispectrum components on a regular grid
* :doc:`sna/grid/local <compute_sna_atom>` - local array of bispectrum components on a regular grid
* :doc:`sna/grid <compute_sna_atom>` - global array of bispectrum components on a regular grid
* :doc:`sna/grid/local <compute_sna_atom>` - local array of bispectrum components on a regular grid
* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
* :doc:`sph/e/atom <compute_sph_e_atom>` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms

10
doc/src/compute_sna_atom.rst
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@ -35,7 +35,7 @@ Syntax
* twojmax = band limit for bispectrum components (non-negative integer)
* R_1, R_2,... = list of cutoff radii, one for each type (distance units)
* w_1, w_2,... = list of neighbor weights, one for each type
* nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
* nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
* zero or more keyword/value pairs may be appended
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner*
@ -223,7 +223,7 @@ These are calculated from the local density of nearby atoms *i'*
around each grid point, as if there was a central atom *i*
at the grid point. This is useful for characterizing fine-scale
structure in a configuration of atoms, and it has been used
to build a machine-learning surrogate for finite-temperature Kohn-Sham
to build a machine-learning surrogate for finite-temperature Kohn-Sham
density functional theory (:ref:`Ellis et al. <Ellis2021>`).
Neighbor atoms not in the group do not contribute to the
bispectrum components of the grid points. The distance cutoff :math:`R_{ii'}`
@ -231,7 +231,7 @@ and other parameters are defined as for a central atom with the same type as the
neighbor atoms *i'*.
Compute *sna/grid* calculates a global array containing bispectrum
components for a regular grid of points.
components for a regular grid of points.
The grid is aligned with the current box dimensions, with the
first point at the box origin, and forming a regular 3d array with
*nx*, *ny*, and *nz* points in the x, y, and z directions. For triclinic
@ -720,7 +720,7 @@ The array contains one row for each of the
:math:`nx \times ny \times nz` grid points, looping over the index for *ix* fastest,
then *iy*, and *iz* slowest. Each row of the array contains the *x*, *y*,
and *z* coordinates of the grid point, followed by the bispectrum
components.
components.
Compute *sna/grid/local* evaluates a local array.
The array contains one row for each of the
@ -754,7 +754,7 @@ The optional keyword defaults are *rmin0* = 0,
.. _Thompson20141:
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316, (2015).
.. _Bartok20101:
**(Bartok)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).

136
src/ML-SNAP/compute_sna_grid.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -41,7 +41,7 @@ ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) :
int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
// skip over arguments used by base class
// so that argument positions are identical to
// so that argument positions are identical to
// regular per-atom compute
arg += nargbase;
@ -63,7 +63,7 @@ ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) :
wselfallflag = 0;
switchinnerflag = 0;
nelements = 1;
// process required arguments
memory->create(radelem,ntypes+1,"sna/grid:radelem"); // offset by 1 to match up with types
@ -175,14 +175,14 @@ ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) :
if (switchinnerflag && !(sinnerflag && dinnerflag))
error->all(FLERR,"Illegal compute sna/grid command: switchinnerflag = 1, missing sinner/dinner keyword");
if (!switchinnerflag && (sinnerflag || dinnerflag))
error->all(FLERR,"Illegal compute sna/grid command: switchinnerflag = 0, unexpected sinner/dinner keyword");
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
nvalues = ncoeff;
@ -236,83 +236,83 @@ void ComputeSNAGrid::compute_array()
const int ntotal = atom->nlocal + atom->nghost;
// insure rij, inside, and typej are of size jnum
snaptr->grow_rij(ntotal);
for (int iz = nzlo; iz <= nzhi; iz++)
for (int iy = nylo; iy <= nyhi; iy++)
for (int ix = nxlo; ix <= nxhi; ix++) {
double xgrid[3];
const int igrid = iz*(nx*ny) + iy*nx + ix;
grid2x(igrid, xgrid);
const double xtmp = xgrid[0];
const double ytmp = xgrid[1];
const double ztmp = xgrid[2];
double xgrid[3];
const int igrid = iz*(nx*ny) + iy*nx + ix;
grid2x(igrid, xgrid);
const double xtmp = xgrid[0];
const double ytmp = xgrid[1];
const double ztmp = xgrid[2];
// currently, all grid points are type 1
const int itype = 1;
int ielem = 0;
if (chemflag)
ielem = map[itype];
const double radi = radelem[itype];
// currently, all grid points are type 1
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
// typej = types of neighbors of I within cutoff
const int itype = 1;
int ielem = 0;
if (chemflag)
ielem = map[itype];
const double radi = radelem[itype];
int ninside = 0;
for (int j = 0; j < ntotal; j++) {
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
// typej = types of neighbors of I within cutoff
// check that j is in compute group
int ninside = 0;
for (int j = 0; j < ntotal; j++) {
if (!(mask[j] & groupbit)) continue;
// check that j is in compute group
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
int jelem = 0;
if (chemflag)
if (!(mask[j] & groupbit)) continue;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
int jelem = 0;
if (chemflag)
jelem = map[jtype];
if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
snaptr->rij[ninside][2] = delz;
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = 2.0*radelem[jtype]*rcutfac;
if (switchinnerflag) {
snaptr->sinnerij[ninside] = sinnerelem[jelem];
snaptr->dinnerij[ninside] = dinnerelem[jelem];
}
if (chemflag) snaptr->element[ninside] = jelem;
ninside++;
}
}
if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
snaptr->rij[ninside][2] = delz;
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = 2.0*radelem[jtype]*rcutfac;
if (switchinnerflag) {
snaptr->sinnerij[ninside] = sinnerelem[jelem];
snaptr->dinnerij[ninside] = dinnerelem[jelem];
}
if (chemflag) snaptr->element[ninside] = jelem;
ninside++;
}
}
snaptr->compute_ui(ninside, ielem);
snaptr->compute_zi();
snaptr->compute_bi(ielem);
snaptr->compute_ui(ninside, ielem);
snaptr->compute_zi();
snaptr->compute_bi(ielem);
// linear contributions
// linear contributions
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
gridlocal[size_array_cols_base+icoeff][iz][iy][ix] = snaptr->blist[icoeff];
// quadratic contributions
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
gridlocal[size_array_cols_base+icoeff][iz][iy][ix] = snaptr->blist[icoeff];
if (quadraticflag) {
int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = snaptr->blist[icoeff];
gridlocal[size_array_cols_base+ncount++][iz][iy][ix] = 0.5*bveci*bveci;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
gridlocal[size_array_cols_base+ncount++][iz][iy][ix] = bveci*snaptr->blist[jcoeff];
}
}
// quadratic contributions
if (quadraticflag) {
int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = snaptr->blist[icoeff];
gridlocal[size_array_cols_base+ncount++][iz][iy][ix] = 0.5*bveci*bveci;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
gridlocal[size_array_cols_base+ncount++][iz][iy][ix] = bveci*snaptr->blist[jcoeff];
}
}
}
memset(&grid[0][0],0,size_array_rows*size_array_cols*sizeof(double));
@ -320,9 +320,9 @@ void ComputeSNAGrid::compute_array()
for (int iz = nzlo; iz <= nzhi; iz++)
for (int iy = nylo; iy <= nyhi; iy++)
for (int ix = nxlo; ix <= nxhi; ix++) {
const int igrid = iz*(nx*ny) + iy*nx + ix;
for (int j = 0; j < nvalues; j++)
grid[igrid][size_array_cols_base + j] = gridlocal[size_array_cols_base + j][iz][iy][ix];
const int igrid = iz*(nx*ny) + iy*nx + ix;
for (int j = 0; j < nvalues; j++)
grid[igrid][size_array_cols_base + j] = gridlocal[size_array_cols_base + j][iz][iy][ix];
}
MPI_Allreduce(&grid[0][0],&gridall[0][0],size_array_rows*size_array_cols,MPI_DOUBLE,MPI_SUM,world);
assign_coords_all();

18
src/ML-SNAP/compute_sna_grid.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -54,19 +54,3 @@ class ComputeSNAGrid : public ComputeGrid {
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
Self-explanatory.
W: More than one compute sna/grid
Self-explanatory.
*/

132
src/ML-SNAP/compute_sna_grid_local.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -41,7 +41,7 @@ ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) :
int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
// skip over arguments used by base class
// so that argument positions are identical to
// so that argument positions are identical to
// regular per-atom compute
arg += nargbase;
@ -63,7 +63,7 @@ ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) :
wselfallflag = 0;
switchinnerflag = 0;
nelements = 1;
// set local input checks
int sinnerflag = 0;
@ -175,14 +175,14 @@ ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) :
if (switchinnerflag && !(sinnerflag && dinnerflag))
error->all(FLERR,"Illegal compute sna/grid/local command: switchinnerflag = 1, missing sinner/dinner keyword");
if (!switchinnerflag && (sinnerflag || dinnerflag))
error->all(FLERR,"Illegal compute sna/grid/local command: switchinnerflag = 0, unexpected sinner/dinner keyword");
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
nvalues = ncoeff;
@ -235,84 +235,84 @@ void ComputeSNAGridLocal::compute_local()
const int ntotal = atom->nlocal + atom->nghost;
// insure rij, inside, and typej are of size jnum
snaptr->grow_rij(ntotal);
int igrid = 0;
for (int iz = nzlo; iz <= nzhi; iz++)
for (int iy = nylo; iy <= nyhi; iy++)
for (int ix = nxlo; ix <= nxhi; ix++) {
double xgrid[3];
grid2x(ix, iy, iz, xgrid);
const double xtmp = xgrid[0];
const double ytmp = xgrid[1];
const double ztmp = xgrid[2];
double xgrid[3];
grid2x(ix, iy, iz, xgrid);
const double xtmp = xgrid[0];
const double ytmp = xgrid[1];
const double ztmp = xgrid[2];
// currently, all grid points are type 1
const int itype = 1;
int ielem = 0;
if (chemflag)
ielem = map[itype];
const double radi = radelem[itype];
// currently, all grid points are type 1
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
// typej = types of neighbors of I within cutoff
const int itype = 1;
int ielem = 0;
if (chemflag)
ielem = map[itype];
const double radi = radelem[itype];
int ninside = 0;
for (int j = 0; j < ntotal; j++) {
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
// typej = types of neighbors of I within cutoff
// check that j is in compute group
int ninside = 0;
for (int j = 0; j < ntotal; j++) {
if (!(mask[j] & groupbit)) continue;
// check that j is in compute group
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
int jelem = 0;
if (chemflag)
jelem = map[jtype];
if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
snaptr->rij[ninside][2] = delz;
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = 2.0*radelem[jtype]*rcutfac;
if (switchinnerflag) {
snaptr->sinnerij[ninside] = sinnerelem[jelem];
snaptr->dinnerij[ninside] = dinnerelem[jelem];
}
if (chemflag) snaptr->element[ninside] = jelem; // element index for multi-element snap
ninside++;
}
}
if (!(mask[j] & groupbit)) continue;
snaptr->compute_ui(ninside, ielem);
snaptr->compute_zi();
snaptr->compute_bi(ielem);
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
int jelem = 0;
if (chemflag)
jelem = map[jtype];
if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
snaptr->rij[ninside][2] = delz;
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = 2.0*radelem[jtype]*rcutfac;
if (switchinnerflag) {
snaptr->sinnerij[ninside] = sinnerelem[jelem];
snaptr->dinnerij[ninside] = dinnerelem[jelem];
}
if (chemflag) snaptr->element[ninside] = jelem; // element index for multi-element snap
ninside++;
}
}
// linear contributions
snaptr->compute_ui(ninside, ielem);
snaptr->compute_zi();
snaptr->compute_bi(ielem);
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
alocal[igrid][size_local_cols_base+icoeff] = snaptr->blist[icoeff];
// linear contributions
// quadratic contributions
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
alocal[igrid][size_local_cols_base+icoeff] = snaptr->blist[icoeff];
if (quadraticflag) {
int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = snaptr->blist[icoeff];
alocal[igrid][size_local_cols_base+ncount++] = 0.5*bveci*bveci;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
alocal[igrid][size_local_cols_base+ncount++] =
bveci*snaptr->blist[jcoeff];
}
}
igrid++;
// quadratic contributions
if (quadraticflag) {
int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = snaptr->blist[icoeff];
alocal[igrid][size_local_cols_base+ncount++] = 0.5*bveci*bveci;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
alocal[igrid][size_local_cols_base+ncount++] =
bveci*snaptr->blist[jcoeff];
}
}
igrid++;
}
}

16
src/ML-SNAP/compute_sna_grid_local.h
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@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -54,17 +54,3 @@ class ComputeSNAGridLocal : public ComputeGridLocal {
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
W: More than one compute sna/grid/local
Self-explanatory.
*/

10
src/compute_grid.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -128,7 +128,7 @@ void ComputeGrid::allocate()
if (nxlo <= nxhi && nylo <= nyhi && nzlo <= nzhi) {
gridlocal_allocated = 1;
memory->create4d_offset(gridlocal,size_array_cols,nzlo,nzhi,nylo,nyhi,
nxlo,nxhi,"grid:gridlocal");
nxlo,nxhi,"grid:gridlocal");
}
array = gridall;
}
@ -179,7 +179,7 @@ void ComputeGrid::set_grid_global()
delxinv = nx/xprd;
delyinv = ny/yprd;
delzinv = nz/zprd;
delx = 1.0/delxinv;
dely = 1.0/delyinv;
delz = 1.0/delzinv;
@ -245,9 +245,9 @@ void ComputeGrid::set_grid_local()
double ComputeGrid::memory_usage()
{
double nbytes = size_array_rows*size_array_cols *
double nbytes = size_array_rows*size_array_cols *
sizeof(double); // grid
nbytes += size_array_rows*size_array_cols *
nbytes += size_array_rows*size_array_cols *
sizeof(double); // gridall
nbytes += size_array_cols*ngridlocal*sizeof(double); // gridlocal
return nbytes;

14
src/compute_grid.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -42,7 +42,7 @@ class ComputeGrid : public Compute {
double *sublo, *subhi; // subdomain info (units real/ortho or reduced/tri)
double delxinv,delyinv,delzinv; // inverse grid spacing
double delx,dely,delz; // grid spacing
int nargbase; // number of base class args
int nargbase; // number of base class args
double cutmax; // largest cutoff distance
int size_array_cols_base; // number of columns used for coords, etc.
int gridlocal_allocated; // shows if gridlocal allocated
@ -59,13 +59,3 @@ class ComputeGrid : public Compute {
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
*/

46
src/compute_grid_local.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -164,7 +164,7 @@ void ComputeGridLocal::set_grid_global()
delxinv = nx/xprd;
delyinv = ny/yprd;
delzinv = nz/zprd;
delx = 1.0/delxinv;
dely = 1.0/delyinv;
delz = 1.0/delzinv;
@ -233,34 +233,34 @@ void ComputeGridLocal::assign_coords()
for (int iz = nzlo; iz <= nzhi; iz++)
for (int iy = nylo; iy <= nyhi; iy++)
for (int ix = nxlo; ix <= nxhi; ix++) {
alocal[igrid][0] = ix;
alocal[igrid][1] = iy;
alocal[igrid][2] = iz;
double xgrid[3];
alocal[igrid][0] = ix;
alocal[igrid][1] = iy;
alocal[igrid][2] = iz;
double xgrid[3];
// for triclinic: create gridpoint in lamda coordinates and transform after check.
// for orthorombic: create gridpoint in box coordinates.
// for triclinic: create gridpoint in lamda coordinates and transform after check.
// for orthorombic: create gridpoint in box coordinates.
if (triclinic)
grid2lamda(ix, iy, iz, xgrid);
else
grid2x(ix, iy, iz, xgrid);
if (triclinic)
grid2lamda(ix, iy, iz, xgrid);
else
grid2x(ix, iy, iz, xgrid);
// ensure gridpoint is not strictly outside subdomain
// ensure gridpoint is not strictly outside subdomain
if ((sublo[0]-xgrid[0]) > EPSILON || (xgrid[0]-subhi[0]) > EPSILON ||
(sublo[1]-xgrid[1]) > EPSILON || (xgrid[1]-subhi[1]) > EPSILON ||
(sublo[2]-xgrid[2]) > EPSILON || (xgrid[2]-subhi[2]) > EPSILON)
error->one(FLERR,"Invalid gridpoint position in compute grid/local");
if ((sublo[0]-xgrid[0]) > EPSILON || (xgrid[0]-subhi[0]) > EPSILON ||
(sublo[1]-xgrid[1]) > EPSILON || (xgrid[1]-subhi[1]) > EPSILON ||
(sublo[2]-xgrid[2]) > EPSILON || (xgrid[2]-subhi[2]) > EPSILON)
error->one(FLERR,"Invalid gridpoint position in compute grid/local");
// convert lamda to x, y, z, after sudomain check
// convert lamda to x, y, z, after sudomain check
if (triclinic) domain->lamda2x(xgrid, xgrid);
if (triclinic) domain->lamda2x(xgrid, xgrid);
alocal[igrid][3] = xgrid[0];
alocal[igrid][4] = xgrid[1];
alocal[igrid][5] = xgrid[2];
igrid++;
alocal[igrid][3] = xgrid[0];
alocal[igrid][4] = xgrid[1];
alocal[igrid][5] = xgrid[2];
igrid++;
}
}

14
src/compute_grid_local.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -39,7 +39,7 @@ class ComputeGridLocal : public Compute {
double *sublo, *subhi; // subdomain info (units real/ortho or reduced/tri)
double delxinv,delyinv,delzinv; // inverse grid spacing
double delx,dely,delz; // grid spacing
int nargbase; // number of base class args
int nargbase; // number of base class args
double cutmax; // largest cutoff distance
int size_local_cols_base; // number of columns used for coords, etc.
int gridlocal_allocated; // shows if gridlocal allocated
@ -57,13 +57,3 @@ class ComputeGridLocal : public Compute {
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
*/