ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6732 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2011-08-18 20:27:57 +00:00
parent dee8b52aa6
commit ade25477f5
6 changed files with 102 additions and 73 deletions
Download Patch File Download Diff File Expand all files Collapse all files

56
src/KSPACE/pppm.cpp
View File

@ -880,7 +880,7 @@ void PPPM::set_grid()
// fluid-occupied volume used to estimate real-space error // fluid-occupied volume used to estimate real-space error
// zprd used rather than zprd_slab // zprd used rather than zprd_slab
double hx,hy,hz; double h_x,h_y,h_z;
if (!gewaldflag) if (!gewaldflag)
g_ewald = sqrt(-log(precision*sqrt(natoms*cutoff*xprd*yprd*zprd) / g_ewald = sqrt(-log(precision*sqrt(natoms*cutoff*xprd*yprd*zprd) /
@ -893,31 +893,31 @@ void PPPM::set_grid()
if (!gridflag) { if (!gridflag) {
double err; double err;
hx = hy = hz = 1/g_ewald; h_x = h_y = h_z = 1/g_ewald;
nx_pppm = static_cast<int> (xprd/hx + 1); nx_pppm = static_cast<int> (xprd/h_x + 1);
ny_pppm = static_cast<int> (yprd/hy + 1); ny_pppm = static_cast<int> (yprd/h_y + 1);
nz_pppm = static_cast<int> (zprd_slab/hz + 1); nz_pppm = static_cast<int> (zprd_slab/h_z + 1);
err = rms(hx,xprd,natoms,q2,acons); err = rms(h_x,xprd,natoms,q2,acons);
while (err > precision) { while (err > precision) {
err = rms(hx,xprd,natoms,q2,acons); err = rms(h_x,xprd,natoms,q2,acons);
nx_pppm++; nx_pppm++;
hx = xprd/nx_pppm; h_x = xprd/nx_pppm;
} }
err = rms(hy,yprd,natoms,q2,acons); err = rms(h_y,yprd,natoms,q2,acons);
while (err > precision) { while (err > precision) {
err = rms(hy,yprd,natoms,q2,acons); err = rms(h_y,yprd,natoms,q2,acons);
ny_pppm++; ny_pppm++;
hy = yprd/ny_pppm; h_y = yprd/ny_pppm;
} }
err = rms(hz,zprd_slab,natoms,q2,acons); err = rms(h_z,zprd_slab,natoms,q2,acons);
while (err > precision) { while (err > precision) {
err = rms(hz,zprd_slab,natoms,q2,acons); err = rms(h_z,zprd_slab,natoms,q2,acons);
nz_pppm++; nz_pppm++;
hz = zprd_slab/nz_pppm; h_z = zprd_slab/nz_pppm;
} }
} }
@ -929,9 +929,9 @@ void PPPM::set_grid()
// adjust g_ewald for new grid size // adjust g_ewald for new grid size
hx = xprd/nx_pppm; h_x = xprd/nx_pppm;
hy = yprd/ny_pppm; h_y = yprd/ny_pppm;
hz = zprd_slab/nz_pppm; h_z = zprd_slab/nz_pppm;
if (!gewaldflag) { if (!gewaldflag) {
double gew1,gew2,dgew,f,fmid,hmin,rtb; double gew1,gew2,dgew,f,fmid,hmin,rtb;
@ -939,12 +939,12 @@ void PPPM::set_grid()
gew1 = 0.0; gew1 = 0.0;
g_ewald = gew1; g_ewald = gew1;
f = diffpr(hx,hy,hz,q2,acons); f = diffpr(h_x,h_y,h_z,q2,acons);
hmin = MIN(hx,MIN(hy,hz)); hmin = MIN(h_x,MIN(h_y,h_z));
gew2 = 10/hmin; gew2 = 10/hmin;
g_ewald = gew2; g_ewald = gew2;
fmid = diffpr(hx,hy,hz,q2,acons); fmid = diffpr(h_x,h_y,h_z,q2,acons);
if (f*fmid >= 0.0) error->all("Cannot compute PPPM G"); if (f*fmid >= 0.0) error->all("Cannot compute PPPM G");
rtb = f < 0.0 ? (dgew=gew2-gew1,gew1) : (dgew=gew1-gew2,gew2); rtb = f < 0.0 ? (dgew=gew2-gew1,gew1) : (dgew=gew1-gew2,gew2);
@ -952,7 +952,7 @@ void PPPM::set_grid()
while (fabs(dgew) > SMALL && fmid != 0.0) { while (fabs(dgew) > SMALL && fmid != 0.0) {
dgew *= 0.5; dgew *= 0.5;
g_ewald = rtb + dgew; g_ewald = rtb + dgew;
fmid = diffpr(hx,hy,hz,q2,acons); fmid = diffpr(h_x,h_y,h_z,q2,acons);
if (fmid <= 0.0) rtb = g_ewald; if (fmid <= 0.0) rtb = g_ewald;
ncount++; ncount++;
if (ncount > LARGE) error->all("Cannot compute PPPM G"); if (ncount > LARGE) error->all("Cannot compute PPPM G");
@ -961,9 +961,9 @@ void PPPM::set_grid()
// final RMS precision // final RMS precision
double lprx = rms(hx,xprd,natoms,q2,acons); double lprx = rms(h_x,xprd,natoms,q2,acons);
double lpry = rms(hy,yprd,natoms,q2,acons); double lpry = rms(h_y,yprd,natoms,q2,acons);
double lprz = rms(hz,zprd_slab,natoms,q2,acons); double lprz = rms(h_z,zprd_slab,natoms,q2,acons);
double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0); double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) / double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd_slab); sqrt(natoms*cutoff*xprd*yprd*zprd_slab);
@ -1038,7 +1038,7 @@ double PPPM::rms(double h, double prd, bigint natoms,
compute difference in real-space and kspace RMS precision compute difference in real-space and kspace RMS precision
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
double PPPM::diffpr(double hx, double hy, double hz, double q2, double **acons) double PPPM::diffpr(double h_x, double h_y, double h_z, double q2, double **acons)
{ {
double lprx,lpry,lprz,kspace_prec,real_prec; double lprx,lpry,lprz,kspace_prec,real_prec;
double xprd = domain->xprd; double xprd = domain->xprd;
@ -1046,9 +1046,9 @@ double PPPM::diffpr(double hx, double hy, double hz, double q2, double **acons)
double zprd = domain->zprd; double zprd = domain->zprd;
bigint natoms = atom->natoms; bigint natoms = atom->natoms;
lprx = rms(hx,xprd,natoms,q2,acons); lprx = rms(h_x,xprd,natoms,q2,acons);
lpry = rms(hy,yprd,natoms,q2,acons); lpry = rms(h_y,yprd,natoms,q2,acons);
lprz = rms(hz,zprd*slab_volfactor,natoms,q2,acons); lprz = rms(h_z,zprd*slab_volfactor,natoms,q2,acons);
kspace_prec = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0); kspace_prec = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
real_prec = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) / real_prec = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(static_cast<double>(natoms)*cutoff*xprd*yprd*zprd); sqrt(static_cast<double>(natoms)*cutoff*xprd*yprd*zprd);

3
src/Makefile
View File

@ -1,6 +1,6 @@
# LAMMPS multiple-machine Makefile # LAMMPS multiple-machine Makefile
SHELL = /bin/sh SHELL = /bin/bash
#.IGNORE: #.IGNORE:
# Definitions # Definitions
@ -68,6 +68,7 @@ help:
@cp -p *.cpp *.h Obj_$@ @cp -p *.cpp *.h Obj_$@
@cp MAKE/Makefile.$@ Obj_$@/Makefile @cp MAKE/Makefile.$@ Obj_$@/Makefile
@if [ ! -e Makefile.package ]; then make package-regenerate; fi @if [ ! -e Makefile.package ]; then make package-regenerate; fi
@if [ ! -e Makefile.package.settings ]; then make package-regenerate; fi
@cp Makefile.package Makefile.package.settings Obj_$@ @cp Makefile.package Makefile.package.settings Obj_$@
@cd Obj_$@; \ @cd Obj_$@; \
$(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" "EXE = ../$(EXE)" ../$(EXE) $(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" "EXE = ../$(EXE)" ../$(EXE)

6
src/REAX/pair_reax_fortran.h
View File

@ -26,10 +26,12 @@
#if __STDC__ #if __STDC__
#define CONS(a,b) a##b #define CONS(a,b) a##b
#elif defined(_IBM)
#define CONS(a,b) a##b
#else #else
#define CONS(a,b) a/**/b #define CONS(a,b) a/**/b
#warning "The following declaration is a test of the CONS macro." #warning "The following declaration is a test of the CONS macro"
#warning "If it fails with an error, pair_reax_fortran.h must be modified by hand." #warning "If it fails, pair_reax_fortran.h must be modified by hand"
static int my_apples_my_oranges = 1; static int my_apples_my_oranges = 1;
static int my_applesoroanges = CONS(my_apples,_my_oranges); static int my_applesoroanges = CONS(my_apples,_my_oranges);
#endif #endif

48
src/USER-CUDA/pppm_cuda.cpp
View File

@ -1305,7 +1305,7 @@ void PPPMCuda::set_grid()
// fluid-occupied volume used to estimate real-space error // fluid-occupied volume used to estimate real-space error
// zprd used rather than zprd_slab // zprd used rather than zprd_slab
double hx,hy,hz; double h_x,h_y,h_z;
if (!gewaldflag) if (!gewaldflag)
g_ewald = sqrt(-log(precision*sqrt(natoms*cutoff*xprd*yprd*zprd) / g_ewald = sqrt(-log(precision*sqrt(natoms*cutoff*xprd*yprd*zprd) /
@ -1318,31 +1318,31 @@ void PPPMCuda::set_grid()
if (!gridflag) { if (!gridflag) {
double err; double err;
hx = hy = hz = 1/g_ewald; h_x = h_y = h_z = 1/g_ewald;
nx_pppm = static_cast<int> (xprd/hx + 1); nx_pppm = static_cast<int> (xprd/h_x + 1);
ny_pppm = static_cast<int> (yprd/hy + 1); ny_pppm = static_cast<int> (yprd/h_y + 1);
nz_pppm = static_cast<int> (zprd_slab/hz + 1); nz_pppm = static_cast<int> (zprd_slab/h_z + 1);
err = rms(hx,xprd,natoms,q2,acons); err = rms(h_x,xprd,natoms,q2,acons);
while (err > precision) { while (err > precision) {
err = rms(hx,xprd,natoms,q2,acons); err = rms(h_x,xprd,natoms,q2,acons);
nx_pppm++; nx_pppm++;
hx = xprd/nx_pppm; h_x = xprd/nx_pppm;
} }
err = rms(hy,yprd,natoms,q2,acons); err = rms(h_y,yprd,natoms,q2,acons);
while (err > precision) { while (err > precision) {
err = rms(hy,yprd,natoms,q2,acons); err = rms(h_y,yprd,natoms,q2,acons);
ny_pppm++; ny_pppm++;
hy = yprd/ny_pppm; h_y = yprd/ny_pppm;
} }
err = rms(hz,zprd_slab,natoms,q2,acons); err = rms(h_z,zprd_slab,natoms,q2,acons);
while (err > precision) { while (err > precision) {
err = rms(hz,zprd_slab,natoms,q2,acons); err = rms(h_z,zprd_slab,natoms,q2,acons);
nz_pppm++; nz_pppm++;
hz = zprd_slab/nz_pppm; h_z = zprd_slab/nz_pppm;
} }
} }
@ -1378,9 +1378,9 @@ void PPPMCuda::set_grid()
// adjust g_ewald for new grid size // adjust g_ewald for new grid size
hx = xprd/nx_pppm; h_x = xprd/nx_pppm;
hy = yprd/ny_pppm; h_y = yprd/ny_pppm;
hz = zprd_slab/nz_pppm; h_z = zprd_slab/nz_pppm;
if (!gewaldflag) { if (!gewaldflag) {
double gew1,gew2,dgew,f,fmid,hmin,rtb; double gew1,gew2,dgew,f,fmid,hmin,rtb;
@ -1388,12 +1388,12 @@ void PPPMCuda::set_grid()
gew1 = 0.0; gew1 = 0.0;
g_ewald = gew1; g_ewald = gew1;
f = diffpr(hx,hy,hz,q2,acons); f = diffpr(h_x,h_y,h_z,q2,acons);
hmin = MIN(hx,MIN(hy,hz)); hmin = MIN(h_x,MIN(h_y,h_z));
gew2 = 10/hmin; gew2 = 10/hmin;
g_ewald = gew2; g_ewald = gew2;
fmid = diffpr(hx,hy,hz,q2,acons); fmid = diffpr(h_x,h_y,h_z,q2,acons);
if (f*fmid >= 0.0) error->all("Cannot compute PPPMCuda G"); if (f*fmid >= 0.0) error->all("Cannot compute PPPMCuda G");
rtb = f < 0.0 ? (dgew=gew2-gew1,gew1) : (dgew=gew1-gew2,gew2); rtb = f < 0.0 ? (dgew=gew2-gew1,gew1) : (dgew=gew1-gew2,gew2);
@ -1401,7 +1401,7 @@ void PPPMCuda::set_grid()
while (fabs(dgew) > SMALL && fmid != 0.0) { while (fabs(dgew) > SMALL && fmid != 0.0) {
dgew *= 0.5; dgew *= 0.5;
g_ewald = rtb + dgew; g_ewald = rtb + dgew;
fmid = diffpr(hx,hy,hz,q2,acons); fmid = diffpr(h_x,h_y,h_z,q2,acons);
if (fmid <= 0.0) rtb = g_ewald; if (fmid <= 0.0) rtb = g_ewald;
ncount++; ncount++;
if (ncount > LARGE) error->all("Cannot compute PPPMCuda G"); if (ncount > LARGE) error->all("Cannot compute PPPMCuda G");
@ -1410,9 +1410,9 @@ void PPPMCuda::set_grid()
// final RMS precision // final RMS precision
double lprx = rms(hx,xprd,natoms,q2,acons); double lprx = rms(h_x,xprd,natoms,q2,acons);
double lpry = rms(hy,yprd,natoms,q2,acons); double lpry = rms(h_y,yprd,natoms,q2,acons);
double lprz = rms(hz,zprd_slab,natoms,q2,acons); double lprz = rms(h_z,zprd_slab,natoms,q2,acons);
double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0); double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) / double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd_slab); sqrt(natoms*cutoff*xprd*yprd*zprd_slab);

2
src/lammps.cpp
View File

@ -325,6 +325,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
if (mpisize != sizeof(bigint)) if (mpisize != sizeof(bigint))
error->all("MPI_LMP_BIGINT and bigint in lmptype.h are not compatible"); error->all("MPI_LMP_BIGINT and bigint in lmptype.h are not compatible");
if (sizeof(tagint) == 8) error->all("64-bit atom IDs are not yet supported");
// create CUDA class if USER-CUDA installed, unless explicitly switched off // create CUDA class if USER-CUDA installed, unless explicitly switched off
// instantiation creates dummy CUDA class if USER-CUDA is not installed // instantiation creates dummy CUDA class if USER-CUDA is not installed

60
src/lmptype.h
View File

@ -19,16 +19,11 @@
// smallint must be an int, as defined by C compiler // smallint must be an int, as defined by C compiler
// tagint can be 32-bit or 64-bit int, must be >= smallint // tagint can be 32-bit or 64-bit int, must be >= smallint
// NOTE: 64-bit tagint is not yet supported
// bigint can be 32-bit or 64-bit int, must be >= tagint // bigint can be 32-bit or 64-bit int, must be >= tagint
// MPI_LMP_TAGINT = MPI data type corresponding to a tagint // MPI_LMP_TAGINT = MPI data type corresponding to a tagint
// MPI_LMP_BIGINT = MPI data type corresponding to a bigint // MPI_LMP_BIGINT = MPI data type corresponding to a bigint
// NOTE: if your machine/MPI does not support "long long" ints,
// but only "long" ints, then you will need to change
// MPI_LONG_LONG to MPI_LONG, and atoll to atol
#ifndef LMP_LMPTYPE_H #ifndef LMP_LMPTYPE_H
#define LMP_LMPTYPE_H #define LMP_LMPTYPE_H
@ -39,6 +34,12 @@
#include "stdint.h" #include "stdint.h"
#include "inttypes.h" #include "inttypes.h"
// grrr - IBM Power6 does not provide this def in their system header files
#ifndef PRId64
#define PRId64 "ld"
#endif
namespace LAMMPS_NS { namespace LAMMPS_NS {
// reserve 2 hi bits in molecular system neigh list for special bonds flag // reserve 2 hi bits in molecular system neigh list for special bonds flag
@ -47,9 +48,27 @@ namespace LAMMPS_NS {
#define SBBITS 30 #define SBBITS 30
#define NEIGHMASK 0x3FFFFFFF #define NEIGHMASK 0x3FFFFFFF
// default settings // default to 32-bit smallint and tagint, 64-bit bigint
#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG)
#define LAMMPS_SMALLBIG
#endif
// allow user override of LONGLONG to LONG, necessary for some machines/MPI
#ifdef LAMMPS_LONGLONG_TO_LONG
#define MPI_LL MPI_LONG
#define ATOLL atoll
#else
#define MPI_LL MPI_LONG_LONG
#define ATOLL atol
#endif
// for atomic problems that exceed 2 billion (2^31) atoms
// 32-bit smallint and tagint, 64-bit bigint // 32-bit smallint and tagint, 64-bit bigint
#ifdef LAMMPS_SMALLBIG
typedef int smallint; typedef int smallint;
typedef int tagint; typedef int tagint;
typedef int64_t bigint; typedef int64_t bigint;
@ -59,19 +78,21 @@ typedef int64_t bigint;
#define MAXBIGINT INT64_MAX #define MAXBIGINT INT64_MAX
#define MPI_LMP_TAGINT MPI_INT #define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_BIGINT MPI_LONG_LONG #define MPI_LMP_BIGINT MPI_LL
#define TAGINT_FORMAT "%d" #define TAGINT_FORMAT "%d"
#define BIGINT_FORMAT "%" PRId64 #define BIGINT_FORMAT "%" PRId64
#define ATOTAGINT atoi #define ATOTAGINT atoi
#define ATOBIGINT atoll #define ATOBIGINT ATOLL
#endif
// for molecular problems that exceed 2 billion (2^31) atoms // for molecular problems that exceed 2 billion (2^31) atoms
// 32-bit smallint, 64-bit tagint and bigint // 32-bit smallint, 64-bit tagint and bigint
// NOTE: 64-bit tagint is not yet supported
/* #ifdef LAMMPS_BIGBIG
typedef int smallint; typedef int smallint;
typedef int64_t tagint; typedef int64_t tagint;
typedef int64_t bigint; typedef int64_t bigint;
@ -80,20 +101,22 @@ typedef int64_t bigint;
#define MAXTAGINT INT64_MAX #define MAXTAGINT INT64_MAX
#define MAXBIGINT INT64_MAX #define MAXBIGINT INT64_MAX
#define MPI_LMP_TAGINT MPI_LONG_LONG #define MPI_LMP_TAGINT MPI_LL
#define MPI_LMP_BIGINT MPI_LONG_LONG #define MPI_LMP_BIGINT MPI_LL
#define TAGINT_FORMAT "%" PRId64 #define TAGINT_FORMAT "%" PRId64
#define BIGINT_FORMAT "%" PRId64 #define BIGINT_FORMAT "%" PRId64
#define ATOTAGINT atoll #define ATOTAGINT ATOLL
#define ATOBIGINT atoll #define ATOBIGINT ATOLL
*/
#endif
// for machines that do not support 64-bit ints // for machines that do not support 64-bit ints
// 32-bit smallint and tagint and bigint // 32-bit smallint and tagint and bigint
/* #ifdef LAMMPS_SMALLSMALL
typedef int smallint; typedef int smallint;
typedef int tagint; typedef int tagint;
typedef int bigint; typedef int bigint;
@ -110,11 +133,12 @@ typedef int bigint;
#define ATOTAGINT atoi #define ATOTAGINT atoi
#define ATOBIGINT atoi #define ATOBIGINT atoi
*/
#endif
} }
// settings to enable LAMMPS build under Windows // settings to enable LAMMPS to build under Windows
#ifdef _WIN32 #ifdef _WIN32
#include "lmpwindows.h" #include "lmpwindows.h"