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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7858 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-02-28 19:52:12 +00:00
parent 00944a2b95
commit 6a544be9cf
7 changed files with 1159 additions and 813 deletions
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43
src/KSPACE/pppm.cpp
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@ -60,8 +60,8 @@ PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
{
if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm command");
precision = atof(arg[0]);
accuracy_relative = atof(arg[0]);
nfactors = 3;
factors = new int[nfactors];
factors[0] = 2;
@ -222,6 +222,11 @@ void PPPM::init()
error->warning(FLERR,str);
}
// set accuracy (force units) from accuracy_relative or accuracy_absolute
if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute;
else accuracy = accuracy_relative * two_charge_force;
// setup FFT grid resolution and g_ewald
// normally one iteration thru while loop is all that is required
// if grid stencil extends beyond neighbor proc, reduce order and try again
@ -229,7 +234,6 @@ void PPPM::init()
int iteration = 0;
while (order > 0) {
if (iteration && me == 0)
error->warning(FLERR,"Reducing PPPM order b/c stencil extends "
"beyond neighbor processor");
@ -970,9 +974,7 @@ void PPPM::set_grid()
acons[7][5] = 1755948832039.0 / 36229939200000.0;
acons[7][6] = 4887769399.0 / 37838389248.0;
//double q2 = qsqsum * force->qqrd2e / force->dielectric;
double q2 = qsqsum / force->dielectric;
bigint natoms = atom->natoms;
double q2 = qsqsum * force->qqrd2e / force->dielectric;
// use xprd,yprd,zprd even if triclinic so grid size is the same
// adjust z dimension for 2d slab PPPM
@ -984,20 +986,21 @@ void PPPM::set_grid()
double zprd_slab = zprd*slab_volfactor;
// make initial g_ewald estimate
// based on desired error and real space cutoff
// based on desired accuracy and real space cutoff
// fluid-occupied volume used to estimate real-space error
// zprd used rather than zprd_slab
double h_x,h_y,h_z;
bigint natoms = atom->natoms;
if (!gewaldflag)
g_ewald = sqrt(-log(precision*sqrt(natoms*cutoff*xprd*yprd*zprd) /
g_ewald = sqrt(-log(accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) /
(2.0*q2))) / cutoff;
// set optimal nx_pppm,ny_pppm,nz_pppm based on order and precision
// set optimal nx_pppm,ny_pppm,nz_pppm based on order and accuracy
// nz_pppm uses extended zprd_slab instead of zprd
// h = 1/g_ewald is upper bound on h such that h*g_ewald <= 1
// reduce it until precision target is met
// reduce it until accuracy target is met
if (!gridflag) {
double err;
@ -1008,21 +1011,21 @@ void PPPM::set_grid()
nz_pppm = static_cast<int> (zprd_slab/h_z + 1);
err = rms(h_x,xprd,natoms,q2,acons);
while (err > precision) {
while (err > accuracy) {
err = rms(h_x,xprd,natoms,q2,acons);
nx_pppm++;
h_x = xprd/nx_pppm;
}
err = rms(h_y,yprd,natoms,q2,acons);
while (err > precision) {
while (err > accuracy) {
err = rms(h_y,yprd,natoms,q2,acons);
ny_pppm++;
h_y = yprd/ny_pppm;
}
err = rms(h_z,zprd_slab,natoms,q2,acons);
while (err > precision) {
while (err > accuracy) {
err = rms(h_z,zprd_slab,natoms,q2,acons);
nz_pppm++;
h_z = zprd_slab/nz_pppm;
@ -1067,7 +1070,7 @@ void PPPM::set_grid()
}
}
// final RMS precision
// final RMS accuracy
double lprx = rms(h_x,xprd,natoms,q2,acons);
double lpry = rms(h_y,yprd,natoms,q2,acons);
@ -1092,14 +1095,18 @@ void PPPM::set_grid()
fprintf(screen," G vector (1/distance)= %g\n",g_ewald);
fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
fprintf(screen," stencil order = %d\n",order);
fprintf(screen," RMS precision = %g\n",MAX(lpr,spr));
fprintf(screen," absolute RMS force accuracy = %g\n",MAX(lpr,spr));
fprintf(screen," relative force accuracy = %g\n",
MAX(lpr,spr)/two_charge_force);
fprintf(screen," using %s precision FFTs\n",fft_prec);
}
if (logfile) {
fprintf(logfile," G vector (1/distance) = %g\n",g_ewald);
fprintf(logfile," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
fprintf(logfile," stencil order = %d\n",order);
fprintf(logfile," RMS precision = %g\n",MAX(lpr,spr));
fprintf(logfile," absolute RMS force accuracy = %g\n",MAX(lpr,spr));
fprintf(logfile," relative force accuracy = %g\n",
MAX(lpr,spr)/two_charge_force);
fprintf(logfile," using %s precision FFTs\n",fft_prec);
}
}
@ -1128,7 +1135,7 @@ int PPPM::factorable(int n)
}
/* ----------------------------------------------------------------------
compute RMS precision for a dimension
compute RMS accuracy for a dimension
------------------------------------------------------------------------- */
double PPPM::rms(double h, double prd, bigint natoms,
@ -1143,7 +1150,7 @@ 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 accuracy
------------------------------------------------------------------------- */
double PPPM::diffpr(double h_x, double h_y, double h_z, double q2,

3
src/KSPACE/pppm.h
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@ -47,7 +47,6 @@ class PPPM : public KSpace {
protected:
int me,nprocs;
double precision;
int nfactors;
int *factors;
double qsum,qsqsum;
@ -221,7 +220,7 @@ E: PPPM grid is too large
The global PPPM grid is larger than OFFSET in one or more dimensions.
OFFSET is currently set to 4096. You likely need to decrease the
requested precision.
requested accuracy.
E: PPPM order has been reduced to 0

1733
src/USER-EWALDN/ewald_n.cpp
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File diff suppressed because it is too large Load Diff

173
src/USER-EWALDN/ewald_n.h
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@ -1,82 +1,91 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef KSPACE_CLASS
KSpaceStyle(ewald/n,EwaldN)
#else
#ifndef LMP_EWALD_N_H
#define LMP_EWALD_N_H
#include "kspace.h"
#include "math_complex.h"
namespace LAMMPS_NS {
#define EWALD_NORDER 6
#define EWALD_NFUNCS 4
#define EWALD_MAX_NSUMS 10
#define EWALD_NSUMS {1, 1, 7, 1}
typedef struct cvector { complex x, y, z; } cvector;
typedef struct hvector { double x, y, z; } hvector;
typedef struct kvector { long x, y, z; } kvector;
class EwaldN : public KSpace {
public:
EwaldN(class LAMMPS *, int, char **);
~EwaldN();
void init();
void setup();
void compute(int, int);
double memory_usage() {return bytes;}
private:
double unit[6];
int function[EWALD_NFUNCS], first_output;
int nkvec, nkvec_max, nevec, nevec_max,
nbox, nfunctions, nsums, sums;
double bytes;
double precision, g2_max;
double *kenergy, energy_self[EWALD_NFUNCS];
double *kvirial, virial_self[EWALD_NFUNCS];
cvector *ekr_local;
hvector *hvec;
kvector *kvec;
double mumurd2e, dielectric, *B, volume;
struct Sum { double x, x2; } sum[EWALD_MAX_NSUMS];
complex *cek_local, *cek_global;
void reallocate();
void reallocate_atoms();
void deallocate();
void coefficients();
void init_coeffs();
void init_coeff_sums();
void init_self();
void compute_ek();
void compute_force();
void compute_surface();
void compute_energy(int);
void compute_virial(int);
void compute_slabcorr(int);
};
}
#endif
#endif
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef KSPACE_CLASS
KSpaceStyle(ewald/n,EwaldN)
#else
#ifndef LMP_EWALD_N_H
#define LMP_EWALD_N_H
#include "kspace.h"
#include "math_complex.h"
namespace LAMMPS_NS {
#define EWALD_NORDER 6
#define EWALD_NFUNCS 4
#define EWALD_MAX_NSUMS 10
#define EWALD_NSUMS {1, 1, 7, 1}
typedef struct cvector { complex x, y, z; } cvector;
typedef struct hvector { double x, y, z; } hvector;
typedef struct kvector { long x, y, z; } kvector;
class EwaldN : public KSpace {
public:
EwaldN(class LAMMPS *, int, char **);
~EwaldN();
void init();
void setup();
void compute(int, int);
double memory_usage() {return bytes;}
private:
double unit[6];
int function[EWALD_NFUNCS], first_output;
int nkvec, nkvec_max, nevec, nevec_max,
nbox, nfunctions, nsums, sums;
int peratom_allocate_flag;
double bytes;
double precision, g2_max;
double *kenergy, energy_self[EWALD_NFUNCS];
double *kvirial, virial_self[EWALD_NFUNCS];
double **energy_self_peratom;
double **virial_self_peratom;
cvector *ekr_local;
hvector *hvec;
kvector *kvec;
double mumurd2e, dielectric, *B, volume;
struct Sum { double x, x2; } sum[EWALD_MAX_NSUMS];
complex *cek_local, *cek_global;
void reallocate();
void allocate_peratom();
void reallocate_atoms();
void deallocate();
void deallocate_peratom();
void coefficients();
void init_coeffs();
void init_coeff_sums();
void init_self();
void init_self_peratom();
void compute_ek();
void compute_force();
void compute_surface();
void compute_surface_peratom();
void compute_energy();
void compute_energy_peratom();
void compute_virial();
void compute_virial_peratom();
void compute_slabcorr();
};
}
#endif
#endif

3
src/fix_box_relax.cpp
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@ -324,7 +324,8 @@ void FixBoxRelax::init()
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all(FLERR,"Pressure ID for fix box/relax does not exist");
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix box/relax does not exist");
pressure = modify->compute[icompute];
pv2e = 1.0 / force->nktv2p;

10
src/kspace.cpp
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@ -16,6 +16,7 @@
#include "kspace.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
@ -32,6 +33,11 @@ KSpace::KSpace(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
slabflag = 0;
slab_volfactor = 1;
accuracy_absolute = -1.0;
two_charge_force = force->qqr2e *
(force->qelectron * force->qelectron) /
(force->angstrom * force->angstrom);
maxeatom = maxvatom = 0;
eatom = NULL;
vatom = NULL;
@ -121,6 +127,10 @@ void KSpace::modify_params(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
order = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"force") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
accuracy_absolute = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"gewald") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
g_ewald = atof(arg[iarg+1]);

7
src/kspace.h
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@ -45,6 +45,13 @@ class KSpace : protected Pointers {
int slabflag;
double scale;
double slab_volfactor;
double accuracy; // accuracy of KSpace solver (force units)
double accuracy_absolute; // user-specifed accuracy in force units
double accuracy_relative; // user-specified dimensionless accuracy
// accurary = acc_rel * two_charge_force
double two_charge_force; // force in user units of two point
// charges separated by 1 Angstrom
int evflag,evflag_atom;
int eflag_either,eflag_global,eflag_atom;