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Copy pathsetup.cpp
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650 lines (510 loc) · 13.8 KB
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/* ----------------------------------------------------------------------
miniMD is a simple, parallel molecular dynamics (MD) code. miniMD is
an MD microapplication in the Mantevo project at Sandia National
Laboratories ( http://www.mantevo.org ). The primary
authors of miniMD are Steve Plimpton (sjplimp@sandia.gov), Paul Crozier
(pscrozi@sandia.gov) and Christian Trott (crtrott@sandia.gov).
Copyright (2008) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This library is free software; you
can redistribute it and/or modify it under the terms of the GNU Lesser
General Public License as published by the Free Software Foundation;
either version 3 of the License, or (at your option) any later
version.
This library is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this software; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
USA. See also: http://www.gnu.org/licenses/lgpl.txt .
For questions, contact Paul S. Crozier (pscrozi@sandia.gov) or
Christian Trott (crtrott@sandia.gov).
Please read the accompanying README and LICENSE files.
---------------------------------------------------------------------- */
#include "atom.h"
#include "integrate.h"
#include "miniMD_math.h"
#include "mpi.h"
#include "neighbor.h"
#include "offload.h"
#include "thermo.h"
#include "types.h"
#include <cstdio>
#include <cstring>
#define MIN(a, b) ((a) < (b) ? (a) : (b))
#define MAX(a, b) ((a) > (b) ? (a) : (b))
double random(int *);
#define NSECTIONS 3
#define MAXLINE 255
char line[MAXLINE];
char keyword[MAXLINE];
FILE *fp;
void read_lammps_parse_keyword(int first)
{
int eof = 0;
char buffer[MAXLINE];
// proc 0 reads upto non-blank line plus 1 following line
// eof is set to 1 if any read hits end-of-file
if(!first)
{
if(fgets(line, MAXLINE, fp) == NULL)
{
eof = 1;
}
}
while(eof == 0 && strspn(line, " \t\n\r") == strlen(line))
{
if(fgets(line, MAXLINE, fp) == NULL)
{
eof = 1;
}
}
if(fgets(buffer, MAXLINE, fp) == NULL)
{
eof = 1;
}
// if eof, set keyword empty and return
if(eof)
{
keyword[0] = '\0';
return;
}
// bcast keyword line to all procs
// copy non-whitespace portion of line into keyword
int start = strspn(line, " \t\n\r");
int stop = strlen(line) - 1;
while(line[stop] == ' ' || line[stop] == '\t' || line[stop] == '\n' || line[stop] == '\r')
{
stop--;
}
line[stop + 1] = '\0';
strcpy(keyword, &line[start]);
}
void read_lammps_header(Atom &atom)
{
int n;
char *ptr;
// customize for new sections
const char *section_keywords[NSECTIONS] = {"Atoms", "Velocities", "Masses"};
// skip 1st line of file
char *eof = fgets(line, MAXLINE, fp);
// customize for new header lines
int ntypes = 0;
while(1)
{
if(fgets(line, MAXLINE, fp) == NULL)
{
n = 0;
}
else
{
n = strlen(line) + 1;
}
if(n == 0)
{
line[0] = '\0';
return;
}
// trim anything from '#' onward
// if line is blank, continue
double xlo, xhi, ylo, yhi, zlo, zhi;
if(ptr == strchr(line, '#'))
{
*ptr = '\0';
}
if(strspn(line, " \t\n\r") == strlen(line))
{
continue;
}
// search line for header keyword and set corresponding variable
if(strstr(line, "atoms"))
{
sscanf(line, "%i", &atom.natoms);
}
else if(strstr(line, "atom types"))
{
sscanf(line, "%i", &ntypes);
// check for these first
// otherwise "triangles" will be matched as "angles"
}
else if(strstr(line, "xlo xhi"))
{
sscanf(line, "%lg %lg", &xlo, &xhi);
atom.box.xprd = xhi - xlo;
}
else if(strstr(line, "ylo yhi"))
{
sscanf(line, "%lg %lg", &ylo, &yhi);
atom.box.yprd = yhi - ylo;
}
else if(strstr(line, "zlo zhi"))
{
sscanf(line, "%lg %lg", &zlo, &zhi);
atom.box.zprd = zhi - zlo;
}
else
{
break;
}
}
// error check on total system size
// check that exiting string is a valid section keyword
read_lammps_parse_keyword(1);
for(n = 0; n < NSECTIONS; n++)
{
if(strcmp(keyword, section_keywords[n]) == 0)
{
break;
}
}
if(n == NSECTIONS)
{
char str[128];
sprintf(str, "Unknown identifier in data file: %s", keyword);
}
// error check on consistency of header values
}
void read_lammps_atoms(Atom &atom, MMD_float *x)
{
int i;
int nread = 0;
int natoms = atom.natoms;
atom.nlocal = 0;
int type;
double xx, xy, xz;
while(nread < natoms)
{
fgets(line, MAXLINE, fp);
sscanf(line, "%i %i %lg %lg %lg", &i, &type, &xx, &xy, &xz);
i--;
x[i * PAD + 0] = xx;
x[i * PAD + 1] = xy;
x[i * PAD + 2] = xz;
nread++;
}
}
void read_lammps_velocities(Atom &atom, MMD_float *v)
{
int i;
int nread = 0;
int natoms = atom.natoms;
double x, y, z;
while(nread < natoms)
{
fgets(line, MAXLINE, fp);
sscanf(line, "%i %lg %lg %lg", &i, &x, &y, &z);
i--;
v[i * PAD + 0] = x;
v[i * PAD + 1] = y;
v[i * PAD + 2] = z;
nread++;
}
// check that all atoms were assigned correctly
}
int read_lammps_data(Atom &atom, Comm &comm, Neighbor &neighbor, Integrate &integrate, Thermo &thermo, char *file, int units)
{
fp = fopen(file, "r");
if(fp == NULL)
{
char str[128];
sprintf(str, "Cannot open file %s", file);
}
read_lammps_header(atom);
comm.setup(neighbor.cutneigh, atom);
if(neighbor.nbinx < 0)
{
MMD_float volume = atom.box.xprd * atom.box.yprd * atom.box.zprd;
MMD_float rho = 1.0 * atom.natoms / volume;
MMD_float neigh_bin_size = pow(rho * 16, MMD_float(1.0 / 3.0));
neighbor.nbinx = atom.box.xprd / neigh_bin_size;
neighbor.nbiny = atom.box.yprd / neigh_bin_size;
neighbor.nbinz = atom.box.zprd / neigh_bin_size;
}
if(neighbor.nbinx == 0)
{
neighbor.nbinx = 1;
}
if(neighbor.nbiny == 0)
{
neighbor.nbiny = 1;
}
if(neighbor.nbinz == 0)
{
neighbor.nbinz = 1;
}
neighbor.setup(atom);
integrate.setup();
// force->setup();
thermo.setup(atom.box.xprd * atom.box.yprd * atom.box.zprd / atom.natoms, integrate, atom, units);
MMD_float *x = ( MMD_float * )mmd_alloc(atom.natoms * PAD * sizeof(MMD_float));
MMD_float *v = ( MMD_float * )mmd_alloc(atom.natoms * PAD * sizeof(MMD_float));
int atomflag = 0;
int tmp;
while(strlen(keyword))
{
if(strcmp(keyword, "Atoms") == 0)
{
read_lammps_atoms(atom, x);
atomflag = 1;
}
else if(strcmp(keyword, "Velocities") == 0)
{
if(atomflag == 0)
{
printf("Must read Atoms before Velocities\n");
}
read_lammps_velocities(atom, v);
}
else if(strcmp(keyword, "Masses") == 0)
{
fgets(line, MAXLINE, fp);
#if PRECISION == 1
sscanf(line, "%i %g", &tmp, &atom.mass);
#else
sscanf(line, "%i %lg", &tmp, &atom.mass);
#endif
}
read_lammps_parse_keyword(0);
}
for(int i = 0; i < atom.natoms; i++)
{
if(x[i * PAD + 0] >= atom.box.xlo && x[i * PAD + 0] < atom.box.xhi && x[i * PAD + 1] >= atom.box.ylo && x[i * PAD + 1] < atom.box.yhi && x[i * PAD + 2] >= atom.box.zlo && x[i * PAD + 2] < atom.box.zhi)
{
atom.addatom(x[i * PAD + 0], x[i * PAD + 1], x[i * PAD + 2], v[i * PAD + 0], v[i * PAD + 1], v[i * PAD + 2]);
}
}
mmd_free(v);
mmd_free(x);
int me;
MPI_Comm_rank(MPI_COMM_WORLD, &me);
/* check that correct # of atoms were created */
int natoms;
MPI_Allreduce(&atom.nlocal, &natoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
if(natoms != atom.natoms)
{
if(me == 0)
{
printf("Created incorrect # of atoms\n");
}
return 1;
}
// check that all atoms were assigned correctly
return 0;
}
/* create simulation box */
void create_box(Atom &atom, int nx, int ny, int nz, double rho)
{
double lattice = pow((4.0 / rho), (1.0 / 3.0));
atom.box.xprd = nx * lattice;
atom.box.yprd = ny * lattice;
atom.box.zprd = nz * lattice;
}
/* initialize atoms on fcc lattice in parallel fashion */
int create_atoms(Atom &atom, int nx, int ny, int nz, double rho)
{
/* total # of atoms */
atom.natoms = 4 * nx * ny * nz;
atom.nlocal = 0;
/* determine loop bounds of lattice subsection that overlaps my sub-box
insure loop bounds do not exceed nx,ny,nz */
double alat = pow((4.0 / rho), (1.0 / 3.0));
int ilo = static_cast<int>(atom.box.xlo / (0.5 * alat) - 1);
int ihi = static_cast<int>(atom.box.xhi / (0.5 * alat) + 1);
int jlo = static_cast<int>(atom.box.ylo / (0.5 * alat) - 1);
int jhi = static_cast<int>(atom.box.yhi / (0.5 * alat) + 1);
int klo = static_cast<int>(atom.box.zlo / (0.5 * alat) - 1);
int khi = static_cast<int>(atom.box.zhi / (0.5 * alat) + 1);
ilo = MAX(ilo, 0);
ihi = MIN(ihi, 2 * nx - 1);
jlo = MAX(jlo, 0);
jhi = MIN(jhi, 2 * ny - 1);
klo = MAX(klo, 0);
khi = MIN(khi, 2 * nz - 1);
/* each proc generates positions and velocities of atoms on fcc sublattice
that overlaps its box
only store atoms that fall in my box
use atom # (generated from lattice coords) as unique seed to generate a
unique velocity
exercise RNG between calls to avoid correlations in adjacent atoms */
double xtmp, ytmp, ztmp, vx, vy, vz;
int i, j, k, m, n;
int sx = 0;
int sy = 0;
int sz = 0;
int ox = 0;
int oy = 0;
int oz = 0;
int subboxdim = 8;
int iflag = 0;
while(oz * subboxdim <= khi)
{
k = oz * subboxdim + sz;
j = oy * subboxdim + sy;
i = ox * subboxdim + sx;
if(iflag)
{
continue;
}
if(((i + j + k) % 2 == 0) && (i >= ilo) && (i <= ihi) && (j >= jlo) && (j <= jhi) && (k >= klo) && (k <= khi))
{
xtmp = 0.5 * alat * i;
ytmp = 0.5 * alat * j;
ztmp = 0.5 * alat * k;
if(xtmp >= atom.box.xlo && xtmp < atom.box.xhi && ytmp >= atom.box.ylo && ytmp < atom.box.yhi && ztmp >= atom.box.zlo && ztmp < atom.box.zhi)
{
n = k * (2 * ny) * (2 * nx) + j * (2 * nx) + i + 1;
for(m = 0; m < 5; m++)
{
random(&n);
}
vx = random(&n);
for(m = 0; m < 5; m++)
{
random(&n);
}
vy = random(&n);
for(m = 0; m < 5; m++)
{
random(&n);
}
vz = random(&n);
atom.addatom(xtmp, ytmp, ztmp, vx, vy, vz);
}
}
sx++;
if(sx == subboxdim)
{
sx = 0;
sy++;
}
if(sy == subboxdim)
{
sy = 0;
sz++;
}
if(sz == subboxdim)
{
sz = 0;
ox++;
}
if(ox * subboxdim > ihi)
{
ox = 0;
oy++;
}
if(oy * subboxdim > jhi)
{
oy = 0;
oz++;
}
}
/* check for overflows on any proc */
int me;
MPI_Comm_rank(MPI_COMM_WORLD, &me);
int iflagall;
MPI_Allreduce(&iflag, &iflagall, 1, MPI_INT, MPI_MAX, MPI_COMM_WORLD);
if(iflagall)
{
if(me == 0)
{
printf("No memory for atoms\n");
}
return 1;
}
/* check that correct # of atoms were created */
int natoms;
MPI_Allreduce(&atom.nlocal, &natoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
if(natoms != atom.natoms)
{
if(me == 0)
{
printf("Created incorrect # of atoms\n");
}
return 1;
}
return 0;
}
/* adjust initial velocities to give desired temperature */
void create_velocity(double t_request, Atom &atom, Thermo &thermo)
{
int i;
/* zero center-of-mass motion */
double vxtot = 0.0;
double vytot = 0.0;
double vztot = 0.0;
for(i = 0; i < atom.nlocal; i++)
{
vxtot += atom.v[i * PAD + 0];
vytot += atom.v[i * PAD + 1];
vztot += atom.v[i * PAD + 2];
}
double tmp;
MPI_Allreduce(&vxtot, &tmp, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
vxtot = tmp / atom.natoms;
MPI_Allreduce(&vytot, &tmp, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
vytot = tmp / atom.natoms;
MPI_Allreduce(&vztot, &tmp, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
vztot = tmp / atom.natoms;
for(i = 0; i < atom.nlocal; i++)
{
atom.v[i * PAD + 0] -= vxtot;
atom.v[i * PAD + 1] -= vytot;
atom.v[i * PAD + 2] -= vztot;
}
/* rescale velocities, including old ones */
thermo.t_act = 0;
#ifdef USE_OFFLOAD
const MMD_float *v = atom.v;
// transfer atom velocities here
// we could alternatively do related compute on the device
#pragma omp target update to(v[0:atom.nlocal * PAD])
#endif
double t = thermo.temperature(atom);
double factor = sqrt(t_request / t);
for(i = 0; i < atom.nlocal; i++)
{
atom.v[i * PAD + 0] *= factor;
atom.v[i * PAD + 1] *= factor;
atom.v[i * PAD + 2] *= factor;
}
}
void finalize_setup(const Atom &atom)
{
#ifdef USE_OFFLOAD
const MMD_float *x = atom.x;
const MMD_float *v = atom.v;
const int * type = atom.type;
// transfer atom state
#pragma omp target update to(x[0:atom.nlocal * PAD])
#pragma omp target update to(v[0:atom.nlocal * PAD])
#pragma omp target update to(type[0:atom.nlocal])
#endif
}
/* Park/Miller RNG w/out MASKING, so as to be like f90s version */
#define IA 16807
#define IM 2147483647
#define AM (1.0 / IM)
#define IQ 127773
#define IR 2836
#define MASK 123459876
double random(int *idum)
{
int k;
double ans;
k = (*idum) / IQ;
*idum = IA * (*idum - k * IQ) - IR * k;
if(*idum < 0)
{
*idum += IM;
}
ans = AM * (*idum);
return ans;
}
#undef IA
#undef IM
#undef AM
#undef IQ
#undef IR
#undef MASK