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@332 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2007-02-21 22:21:06 +00:00
parent 1445a6d536
commit dfad2a399c
12 changed files with 495 additions and 164 deletions
Download Patch File Download Diff File Expand all files Collapse all files

218
src/min_cg.cpp
View File

@ -72,12 +72,12 @@ void MinCG::init()
delete [] fixarg;
fix_minimize = (FixMinimize *) modify->fix[modify->nfix-1];
// zero local vectors before first atom exchange
// zero gradient vectors before first atom exchange
set_local_vectors();
setup_vectors();
for (int i = 0; i < ndof; i++) h[i] = g[i] = 0.0;
// virial_thermo = how virial computed on thermo timesteps
// virial_thermo is how virial should be computed on thermo timesteps
// 1 = computed explicity by pair, 2 = computed implicitly by pair
if (force->newton_pair) virial_thermo = 2;
@ -127,31 +127,28 @@ void MinCG::init()
void MinCG::run()
{
int i;
double tmp;
double tmp,*f;
// set initial force & energy
setup();
setup_vectors();
output->thermo->compute_pe();
energy = output->thermo->potential_energy;
energy += energy_extra;
ecurrent = output->thermo->potential_energy;
// stats for Finish to print
einitial = energy;
einitial = ecurrent;
f = atom->f[0];
tmp = 0.0;
for (i = 0; i < ndof; i++) tmp += f[i]*f[i];
for (int i = 0; i < ndof; i++) tmp += f[i]*f[i];
MPI_Allreduce(&tmp,&gnorm2_init,1,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) gnorm2_init += fextra[i]*fextra[i];
gnorm2_init = sqrt(gnorm2_init);
tmp = 0.0;
for (i = 0; i < ndof; i++) tmp = MAX(fabs(f[i]),tmp);
for (int i = 0; i < ndof; i++) tmp = MAX(fabs(f[i]),tmp);
MPI_Allreduce(&tmp,&gnorminf_init,1,MPI_DOUBLE,MPI_MAX,world);
for (i = 0; i < ndof_extra; i++)
gnorminf_init = MAX(gnorminf_init,fabs(fextra[i]));
// minimizer iterations
@ -172,19 +169,16 @@ void MinCG::run()
output->next_dump_any = update->ntimestep;
if (output->restart_every) output->next_restart = update->ntimestep;
output->next_thermo = update->ntimestep;
eng_force();
int ntmp;
double *xtmp,*htmp,etmp;
eng_force(&ntmp,&xtmp,&htmp,&etmp);
output->write(update->ntimestep);
}
timer->barrier_stop(TIME_LOOP);
// delete fix at end of run, so its atom arrays won't persist
// delete extra arrays
modify->delete_fix("MINIMIZE");
delete [] xextra;
delete [] fextra;
delete [] gextra;
delete [] hextra;
// reset reneighboring criteria
@ -194,20 +188,17 @@ void MinCG::run()
// stats for Finish to print
efinal = energy;
efinal = ecurrent;
f = atom->f[0];
tmp = 0.0;
for (i = 0; i < ndof; i++) tmp += f[i]*f[i];
for (int i = 0; i < ndof; i++) tmp += f[i]*f[i];
MPI_Allreduce(&tmp,&gnorm2_final,1,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) gnorm2_final += fextra[i]*fextra[i];
gnorm2_final = sqrt(gnorm2_final);
tmp = 0.0;
for (i = 0; i < ndof; i++) tmp = MAX(fabs(f[i]),tmp);
for (int i = 0; i < ndof; i++) tmp = MAX(fabs(f[i]),tmp);
MPI_Allreduce(&tmp,&gnorminf_final,1,MPI_DOUBLE,MPI_MAX,world);
for (i = 0; i < ndof_extra; i++)
gnorminf_final = MAX(gnorminf_final,fabs(fextra[i]));
}
/* ----------------------------------------------------------------------
@ -216,20 +207,6 @@ void MinCG::run()
void MinCG::setup()
{
// allocate extra arrays
// couldn't do in init(), b/c modify and fixes weren't yet init()
// set initial xextra values via fixes
ndof_extra = modify->min_dof();
xextra = new double[ndof_extra];
fextra = new double[ndof_extra];
gextra = new double[ndof_extra];
hextra = new double[ndof_extra];
modify->min_xinitial(xextra);
// perform usual setup
if (comm->me == 0 && screen) fprintf(screen,"Setting up minimization ...\n");
// setup domain, communication and neighboring
@ -245,7 +222,7 @@ void MinCG::setup()
comm->borders();
neighbor->build();
neighbor->ncalls = 0;
set_local_vectors();
setup_vectors();
// compute all forces
@ -270,7 +247,6 @@ void MinCG::setup()
if (force->newton) comm->reverse_communicate();
modify->setup();
energy_extra = modify->min_energy(xextra,fextra);
output->setup(1);
}
@ -283,14 +259,14 @@ void MinCG::iterate(int n)
{
int i,gradsearch,fail;
double alpha,beta,gg,dot[2],dotall[2];
double *f;
for (i = 0; i < ndof; i++) h[i] = g[i] = f[i];
for (i = 0; i < ndof_extra; i++) hextra[i] = gextra[i] = fextra[i];
f = atom->f[0];
for (int i = 0; i < ndof; i++) h[i] = g[i] = f[i];
dot[0] = 0.0;
for (i = 0; i < ndof; i++) dot[0] += f[i]*f[i];
MPI_Allreduce(dot,&gg,1,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) gg += fextra[i]*fextra[i];
neval = 0;
gradsearch = 1;
@ -301,8 +277,8 @@ void MinCG::iterate(int n)
// line minimization along direction h from current atom->x
eprevious = energy;
fail = (this->*linemin)(neval);
eprevious = ecurrent;
fail = (this->*linemin)(ndof,atom->x[0],h,ecurrent,dmin,dmax,alpha,neval);
// if max_eval exceeded, all done
// if linemin failed or energy did not decrease sufficiently:
@ -311,8 +287,8 @@ void MinCG::iterate(int n)
if (neval >= update->max_eval) break;
if (fail || fabs(energy-eprevious) <=
update->tolerance * 0.5*(fabs(energy) + fabs(eprevious) + EPS)) {
if (fail || fabs(ecurrent-eprevious) <=
update->tolerance * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS)) {
if (gradsearch == 1) break;
gradsearch = -1;
}
@ -323,16 +299,13 @@ void MinCG::iterate(int n)
// force new search dir to be grad dir if need to restart CG
// set gradsearch to 1 if will search in grad dir on next iteration
f = atom->f[0];
dot[0] = dot[1] = 0.0;
for (i = 0; i < ndof; i++) {
dot[0] += f[i]*f[i];
dot[1] += f[i]*g[i];
}
MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) {
dotall[0] += fextra[i]*fextra[i];
dotall[1] += fextra[i]*gextra[i];
}
beta = MAX(0.0,(dotall[0] - dotall[1])/gg);
gg = dotall[0];
@ -346,10 +319,6 @@ void MinCG::iterate(int n)
g[i] = f[i];
h[i] = g[i] + beta*h[i];
}
for (i = 0; i < ndof_extra; i++) {
gextra[i] = fextra[i];
hextra[i] = gextra[i] + beta*hextra[i];
}
// output for thermo, dump, restart files
@ -365,11 +334,9 @@ void MinCG::iterate(int n)
set ndof and vector pointers after atoms have migrated
------------------------------------------------------------------------- */
void MinCG::set_local_vectors()
void MinCG::setup_vectors()
{
ndof = 3 * atom->nlocal;
x = atom->x[0];
f = atom->f[0];
if (ndof) g = fix_minimize->gradient[0];
else g = NULL;
if (ndof) h = fix_minimize->searchdir[0];
@ -379,11 +346,11 @@ void MinCG::set_local_vectors()
/* ----------------------------------------------------------------------
evaluate potential energy and forces
may migrate atoms
energy = new objective function energy = poteng of atoms + eng_extra
atom->f, fextra = negative gradient of objective function
new energy stored in ecurrent and returned (in case caller not in class)
negative gradient will be stored in atom->f
------------------------------------------------------------------------- */
void MinCG::eng_force()
void MinCG::eng_force(int *pndof, double **px, double **ph, double *peng)
{
// check for reneighboring
// always communicate since minimizer moved atoms
@ -408,7 +375,7 @@ void MinCG::eng_force()
timer->stamp(TIME_COMM);
neighbor->build();
timer->stamp(TIME_NEIGHBOR);
set_local_vectors();
setup_vectors();
}
// eflag is always set, since minimizer needs potential energy
@ -442,17 +409,21 @@ void MinCG::eng_force()
timer->stamp(TIME_COMM);
}
// min_post_force = forces on atoms that affect minimization
// min_energy = energy, forces on extra degrees of freedom
// fixes that affect minimization
if (modify->n_min_post_force) modify->min_post_force(vflag);
if (modify->n_min_energy) energy_extra = modify->min_energy(xextra,fextra);
// compute potential energy of system via Thermo
output->thermo->compute_pe();
energy = output->thermo->potential_energy;
energy += energy_extra;
ecurrent = output->thermo->potential_energy;
// return updated ptrs to caller since atoms may have migrated
*pndof = ndof;
*px = atom->x[0];
*ph = h;
*peng = ecurrent;
}
/* ----------------------------------------------------------------------
@ -516,15 +487,25 @@ void MinCG::force_clear(int vflag)
/* ----------------------------------------------------------------------
line minimization methods
find minimum-energy starting at x along h direction
update atom->x by alpha, call eng_force() for result
alpha = distance moved along h to set x to minimun-energy configuration
return 0 if successful move, 1 if failed (no move)
insure last call to eng_force() is consistent with return
find minimum-energy starting at x along dir direction
input: n = # of degrees of freedom on this proc
x = ptr to atom->x[0] as vector
dir = search direction as vector
eng = current energy at initial x
min/max dist = min/max distance to move any atom coord
output: return 0 if successful move, set alpha
return 1 if failed, no move, no need to set alpha
alpha = distance moved along dir to set x to min-eng config
caller has several quantities set via last call to eng_force()
INSURE last call to eng_force() is consistent with returns
if fail, eng_force() of original x
if succeed, eng_force() at x + alpha*h
eng_force() may migrate atoms due to neighbor list build
therefore linemin routines CANNOT store atom-based quantities
if succeed, eng_force() at x + alpha*dir
atom->x = coords at new configuration
atom->f = force (-Grad) is evaulated at new configuration
ecurrent = energy of new configuration
NOTE: when call eng_force: n,x,dir,eng may change due to atom migration
updated values are returned by eng_force()
this routine CANNOT store atom-based quantities b/c of migration
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
@ -534,55 +515,52 @@ void MinCG::force_clear(int vflag)
quit as soon as energy starts to rise
------------------------------------------------------------------------- */
int MinCG::linemin_scan(int &nfunc)
int MinCG::linemin_scan(int n, double *x, double *dir, double eng,
double mindist, double maxdist,
double &alpha, int &nfunc)
{
int i;
double fmax,fme,elowest,alpha,alphamin,alphamax,alphalast;
double fmax,fme,elowest,alphamin,alphamax,alphalast;
// alphamin = step that moves some atom coord by mindist
// alphamax = step that moves some atom coord by maxdist
fme = 0.0;
for (i = 0; i < ndof; i++) fme = MAX(fme,fabs(h[i]));
for (i = 0; i < n; i++) fme = MAX(fme,fabs(dir[i]));
MPI_Allreduce(&fme,&fmax,1,MPI_DOUBLE,MPI_MAX,world);
for (i = 0; i < ndof_extra; i++) fmax = MAX(fmax,fabs(hextra[i]));
if (fmax == 0.0) return 1;
alphamin = dmin/fmax;
alphamax = dmax/fmax;
alphamin = mindist/fmax;
alphamax = maxdist/fmax;
// if minstep is already uphill, fail
// if eng increases, stop and return previous alpha
// if alphamax, stop and return alphamax
elowest = energy;
elowest = eng;
alpha = alphamin;
while (1) {
for (i = 0; i < ndof; i++) x[i] += alpha*h[i];
for (i = 0; i < ndof_extra; i++) xextra[i] += alpha*hextra[i];
eng_force();
for (i = 0; i < n; i++) x[i] += alpha*dir[i];
eng_force(&n,&x,&dir,&eng);
nfunc++;
if (alpha == alphamin && energy >= elowest) {
for (i = 0; i < ndof; i++) x[i] -= alpha*h[i];
for (i = 0; i < ndof_extra; i++) xextra[i] -= alpha*hextra[i];
eng_force();
if (alpha == alphamin && eng >= elowest) {
for (i = 0; i < n; i++) x[i] -= alpha*dir[i];
eng_force(&n,&x,&dir,&eng);
nfunc++;
return 1;
}
if (energy > elowest) {
for (i = 0; i < ndof; i++) x[i] += (alphalast-alpha)*h[i];
for (i = 0; i < ndof_extra; i++)
xextra[i] += (alphalast-alpha)*hextra[i];
eng_force();
if (eng > elowest) {
for (i = 0; i < n; i++) x[i] += (alphalast-alpha)*dir[i];
eng_force(&n,&x,&dir,&eng);
nfunc++;
alpha = alphalast;
return 0;
}
if (alpha == alphamax) return 0;
elowest = energy;
elowest = eng;
alphalast = alpha;
alpha *= SCAN_FACTOR;
if (alpha > alphamax) alpha = alphamax;
@ -596,44 +574,43 @@ int MinCG::linemin_scan(int &nfunc)
prevents successvive func evals further apart in x than maxdist
------------------------------------------------------------------------- */
int MinCG::linemin_secant(int &nfunc)
int MinCG::linemin_secant(int n, double *x, double *dir, double eng,
double mindist, double maxdist,
double &alpha, int &nfunc)
{
int i,iter;
double eta,eta_prev,sigma0,sigmamax,alpha,alphadelta,fme,fmax,dsq,e0,tmp;
double eta,eta_prev,sigma0,sigmamax,alphadelta,fme,fmax,dsq,e0,tmp;
double *f;
double epssq = SECANT_EPS * SECANT_EPS;
// stopping criterion for secant iterations
fme = 0.0;
for (i = 0; i < ndof; i++) fme += h[i]*h[i];
for (i = 0; i < n; i++) fme += dir[i]*dir[i];
MPI_Allreduce(&fme,&dsq,1,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) dsq += hextra[i]*hextra[i];
// sigma0 = smallest allowed step of mindist
// sigmamax = largest allowed step (in single iteration) of maxdist
fme = 0.0;
for (i = 0; i < ndof; i++) fme = MAX(fme,fabs(h[i]));
for (i = 0; i < n; i++) fme = MAX(fme,fabs(dir[i]));
MPI_Allreduce(&fme,&fmax,1,MPI_DOUBLE,MPI_MAX,world);
for (i = 0; i < ndof_extra; i++) fmax = MAX(fmax,fabs(hextra[i]));
if (fmax == 0.0) return 1;
sigma0 = dmin/fmax;
sigmamax = dmax/fmax;
sigma0 = mindist/fmax;
sigmamax = maxdist/fmax;
// eval func at sigma0
// test if minstep is already uphill
e0 = energy;
for (i = 0; i < ndof; i++) x[i] += sigma0*h[i];
for (i = 0; i < ndof_extra; i++) xextra[i] += sigma0*hextra[i];
eng_force();
e0 = eng;
for (i = 0; i < n; i++) x[i] += sigma0*dir[i];
eng_force(&n,&x,&dir,&eng);
nfunc++;
if (energy >= e0) {
for (i = 0; i < ndof; i++) x[i] -= sigma0*h[i];
for (i = 0; i < ndof_extra; i++) xextra[i] -= sigma0*hextra[i];
eng_force();
if (eng >= e0) {
for (i = 0; i < n; i++) x[i] -= sigma0*dir[i];
eng_force(&n,&x,&dir,&eng);
nfunc++;
return 1;
}
@ -641,25 +618,24 @@ int MinCG::linemin_secant(int &nfunc)
// secant iterations
// alphadelta = new increment to move, alpha = accumulated move
f = atom->f[0];
tmp = 0.0;
for (i = 0; i < ndof; i++) tmp -= f[i]*h[i];
for (i = 0; i < n; i++) tmp -= f[i]*dir[i];
MPI_Allreduce(&tmp,&eta_prev,1,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) eta_prev -= fextra[i]*hextra[i];
alpha = sigma0;
alphadelta = -sigma0;
for (iter = 0; iter < lineiter; iter++) {
alpha += alphadelta;
for (i = 0; i < ndof; i++) x[i] += alphadelta*h[i];
for (i = 0; i < ndof_extra; i++) xextra[i] += alphadelta*hextra[i];
eng_force();
for (i = 0; i < n; i++) x[i] += alphadelta*dir[i];
eng_force(&n,&x,&dir,&eng);
nfunc++;
f = atom->f[0];
tmp = 0.0;
for (i = 0; i < ndof; i++) tmp -= f[i]*h[i];
for (i = 0; i < n; i++) tmp -= f[i]*dir[i];
MPI_Allreduce(&tmp,&eta,1,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) eta -= fextra[i]*hextra[i];
alphadelta *= eta / (eta_prev - eta);
eta_prev = eta;

33
src/min_cg.h
View File

@ -28,38 +28,31 @@ class MinCG : public Min {
protected:
int virial_thermo; // what vflag should be on thermo steps (1,2)
int pairflag,torqueflag,granflag; // force clear flags
int pairflag,torqueflag,granflag;
int neigh_every,neigh_delay,neigh_dist_check; // copies of reneigh criteria
int maxpair; // copies of Update quantities
double **f_pair;
class FixMinimize *fix_minimize; // fix that stores gradient vecs
double ecurrent; // current potential energy
double mindist,maxdist; // min/max dist for coord delta in line search
int ndof; // 3N degrees-of-freedom on this proc
double *x; // vec of 3N coords, ptr to atom->x[0]
double *f; // vec of 3N forces, ptr to atom->f[0]
double *g; // vec of 3N old forces, ptr to fix_minimize::g
double *h; // vec of 3N search dir, ptr to fix_minimize::h
int ndof; // # of degrees-of-freedom on this proc
double *g,*h; // local portion of gradient, searchdir vectors
int ndof_extra; // extra degrees of freedom to include in min
double energy_extra; // extra potential energy
double *xextra; // extra vecs associated with ndof_extra
double *fextra;
double *gextra;
double *hextra;
double energy; // potential energy of atoms and extra dof
typedef int (MinCG::*FnPtr)(int &);
typedef int (MinCG::*FnPtr)(int, double *, double *, double,
double, double, double &, int &);
FnPtr linemin; // ptr to linemin functions
int linemin_scan(int &);
int linemin_secant(int &);
int linemin_scan(int, double *, double *, double,
double, double, double &, int &);
int linemin_secant(int, double *, double *, double,
double, double, double &, int &);
void setup();
void set_local_vectors();
void eng_force();
void setup_vectors();
void eng_force(int *, double **, double **, double *);
void force_clear(int);
};

18
src/min_cg_fr.cpp
View File

@ -39,14 +39,14 @@ void MinCGFR::iterate(int n)
{
int i,gradsearch,fail;
double alpha,beta,gg,dot,dotall;
double *f;
f = atom->f[0];
for (int i = 0; i < ndof; i++) h[i] = g[i] = f[i];
for (i = 0; i < ndof_extra; i++) hextra[i] = gextra[i] = fextra[i];
dot = 0.0;
for (i = 0; i < ndof; i++) dot += f[i]*f[i];
MPI_Allreduce(&dot,&gg,1,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) gg += fextra[i]*fextra[i];
neval = 0;
gradsearch = 1;
@ -57,8 +57,8 @@ void MinCGFR::iterate(int n)
// line minimization along direction h from current atom->x
eprevious = energy;
fail = (this->*linemin)(neval);
eprevious = ecurrent;
fail = (this->*linemin)(ndof,atom->x[0],h,ecurrent,dmin,dmax,alpha,neval);
// if max_eval exceeded, all done
// if linemin failed or energy did not decrease sufficiently:
@ -67,8 +67,8 @@ void MinCGFR::iterate(int n)
if (neval >= update->max_eval) break;
if (fail || fabs(energy-eprevious) <=
update->tolerance * 0.5*(fabs(energy) + fabs(eprevious) + EPS)) {
if (fail || fabs(ecurrent-eprevious) <=
update->tolerance * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS)) {
if (gradsearch == 1) break;
gradsearch = -1;
}
@ -79,10 +79,10 @@ void MinCGFR::iterate(int n)
// force new search dir to be grad dir if need to restart CG
// set gradsesarch to 1 if will search in grad dir on next iteration
f = atom->f[0];
dot = 0.0;
for (i = 0; i < ndof; i++) dot += f[i]*f[i];
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) dotall += fextra[i]*fextra[i];
beta = dotall/gg;
gg = dotall;
@ -96,10 +96,6 @@ void MinCGFR::iterate(int n)
g[i] = f[i];
h[i] = g[i] + beta*h[i];
}
for (i = 0; i < ndof_extra; i++) {
gextra[i] = fextra[i];
hextra[i] = gextra[i] + beta*hextra[i];
}
// output for thermo, dump, restart files

14
src/min_sd.cpp
View File

@ -35,9 +35,10 @@ void MinSD::iterate(int n)
{
int i,fail;
double alpha,dot,dotall;
double *f;
f = atom->f[0];
for (int i = 0; i < ndof; i++) h[i] = f[i];
for (i = 0; i < ndof_extra; i++) hextra[i] = fextra[i];
neval = 0;
@ -47,29 +48,28 @@ void MinSD::iterate(int n)
// line minimization along direction h from current atom->x
eprevious = energy;
fail = (this->*linemin)(neval);
eprevious = ecurrent;
fail = (this->*linemin)(ndof,atom->x[0],h,ecurrent,dmin,dmax,alpha,neval);
// if max_eval exceeded, all done
// if linemin failed or energy did not decrease sufficiently, all done
if (neval >= update->max_eval) break;
if (fail || fabs(energy-eprevious) <=
update->tolerance * 0.5*(fabs(energy) + fabs(eprevious) + EPS))
if (fail || fabs(ecurrent-eprevious) <=
update->tolerance * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS))
break;
// set h to new f = -Grad(x)
// done if size sq of grad vector < EPS
f = atom->f[0];
dot = 0.0;
for (i = 0; i < ndof; i++) dot += f[i]*f[i];
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < ndof_extra; i++) dotall += fextra[i]*fextra[i];
if (dotall < EPS) break;
for (i = 0; i < ndof; i++) h[i] = f[i];
for (i = 0; i < ndof_extra; i++) hextra[i] = fextra[i];
// output for thermo, dump, restart files

56
src/style_class2.h
View File

@ -0,0 +1,56 @@
/* ----------------------------------------------------------------------
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 AngleInclude
#include "angle_class2.h"
#endif
#ifdef AngleClass
AngleStyle(class2,AngleClass2)
#endif
#ifdef BondInclude
#include "bond_class2.h"
#endif
#ifdef BondClass
BondStyle(class2,BondClass2)
#endif
#ifdef DihedralInclude
#include "dihedral_class2.h"
#endif
#ifdef DihedralClass
DihedralStyle(class2,DihedralClass2)
#endif
#ifdef ImproperInclude
#include "improper_class2.h"
#endif
#ifdef ImproperClass
ImproperStyle(class2,ImproperClass2)
#endif
#ifdef PairInclude
#include "pair_lj_class2.h"
#include "pair_lj_class2_coul_cut.h"
#include "pair_lj_class2_coul_long.h"
#endif
#ifdef PairClass
PairStyle(lj/class2,PairLJClass2)
PairStyle(lj/class2/coul/cut,PairLJClass2CoulCut)
PairStyle(lj/class2/coul/long,PairLJClass2CoulLong)
#endif

28
src/style_dpd.h
View File

@ -0,0 +1,28 @@
/* ----------------------------------------------------------------------
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 AtomInclude
#include "atom_vec_dpd.h"
#endif
#ifdef AtomClass
AtomStyle(dpd,AtomVecDPD)
#endif
#ifdef PairInclude
#include "pair_dpd.h"
#endif
#ifdef PairClass
PairStyle(dpd,PairDPD)
#endif

50
src/style_granular.h
View File

@ -0,0 +1,50 @@
/* ----------------------------------------------------------------------
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 AtomInclude
#include "atom_vec_granular.h"
#endif
#ifdef AtomClass
AtomStyle(granular,AtomVecGranular)
# endif
#ifdef FixInclude
#include "fix_freeze.h"
#include "fix_gran_diag.h"
#include "fix_nve_gran.h"
#include "fix_pour.h"
#include "fix_shear_history.h"
#include "fix_wall_gran.h"
#endif
#ifdef FixClass
FixStyle(freeze,FixFreeze)
FixStyle(gran/diag,FixGranDiag)
FixStyle(nve/gran,FixNVEGran)
FixStyle(pour,FixPour)
FixStyle(SHEAR_HISTORY,FixShearHistory)
FixStyle(wall/gran,FixWallGran)
#endif
#ifdef PairInclude
#include "pair_gran_hertzian.h"
#include "pair_gran_history.h"
#include "pair_gran_no_history.h"
#endif
#ifdef PairClass
PairStyle(gran/hertzian,PairGranHertzian)
PairStyle(gran/history,PairGranHistory)
PairStyle(gran/no_history,PairGranNoHistory)
#endif

38
src/style_kspace.h
View File

@ -0,0 +1,38 @@
/* ----------------------------------------------------------------------
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 KSpaceInclude
#include "ewald.h"
#include "pppm.h"
#include "pppm_tip4p.h"
#endif
#ifdef KSpaceClass
KSpaceStyle(ewald,Ewald)
KSpaceStyle(pppm,PPPM)
KSpaceStyle(pppm/tip4p,PPPMTIP4P)
#endif
#ifdef PairInclude
#include "pair_buck_coul_long.h"
#include "pair_lj_cut_coul_long.h"
#include "pair_lj_cut_coul_long_tip4p.h"
#include "pair_lj_charmm_coul_long.h"
#endif
#ifdef PairClass
PairStyle(buck/coul/long,PairBuckCoulLong)
PairStyle(lj/cut/coul/long,PairLJCutCoulLong)
PairStyle(lj/cut/coul/long/tip4p,PairLJCutCoulLongTIP4P)
PairStyle(lj/charmm/coul/long,PairLJCharmmCoulLong)
#endif

28
src/style_manybody.h
View File

@ -0,0 +1,28 @@
/* ----------------------------------------------------------------------
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 PairInclude
#include "pair_eam.h"
#include "pair_eam_alloy.h"
#include "pair_eam_fs.h"
#include "pair_sw.h"
#include "pair_tersoff.h"
#endif
#ifdef PairClass
PairStyle(eam,PairEAM)
PairStyle(eam/alloy,PairEAMAlloy)
PairStyle(eam/fs,PairEAMFS)
PairStyle(sw,PairSW)
PairStyle(tersoff,PairTersoff)
#endif

116
src/style_molecule.h
View File

@ -0,0 +1,116 @@
/* ----------------------------------------------------------------------
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 AngleInclude
#include "angle_charmm.h"
#include "angle_cosine.h"
#include "angle_cosine_squared.h"
#include "angle_harmonic.h"
#include "angle_hybrid.h"
#endif
#ifdef AngleClass
AngleStyle(charmm,AngleCharmm)
AngleStyle(cosine,AngleCosine)
AngleStyle(cosine/squared,AngleCosineSquared)
AngleStyle(harmonic,AngleHarmonic)
AngleStyle(hybrid,AngleHybrid)
#endif
#ifdef AtomInclude
#include "atom_vec_angle.h"
#include "atom_vec_bond.h"
#include "atom_vec_full.h"
#include "atom_vec_molecular.h"
#endif
#ifdef AtomClass
AtomStyle(angle,AtomVecAngle)
AtomStyle(bond,AtomVecBond)
AtomStyle(full,AtomVecFull)
AtomStyle(molecular,AtomVecMolecular)
#endif
#ifdef BondInclude
#include "bond_fene.h"
#include "bond_fene_expand.h"
#include "bond_harmonic.h"
#include "bond_hybrid.h"
#include "bond_morse.h"
#include "bond_nonlinear.h"
#include "bond_quartic.h"
#endif
#ifdef BondClass
BondStyle(fene,BondFENE)
BondStyle(fene/expand,BondFENEExpand)
BondStyle(harmonic,BondHarmonic)
BondStyle(hybrid,BondHybrid)
BondStyle(morse,BondMorse)
BondStyle(nonlinear,BondNonlinear)
BondStyle(quartic,BondQuartic)
#endif
#ifdef DihedralInclude
#include "dihedral_charmm.h"
#include "dihedral_harmonic.h"
#include "dihedral_helix.h"
#include "dihedral_hybrid.h"
#include "dihedral_multi_harmonic.h"
#include "dihedral_opls.h"
#endif
#ifdef DihedralClass
DihedralStyle(charmm,DihedralCharmm)
DihedralStyle(harmonic,DihedralHarmonic)
DihedralStyle(helix,DihedralHelix)
DihedralStyle(hybrid,DihedralHybrid)
DihedralStyle(multi/harmonic,DihedralMultiHarmonic)
DihedralStyle(opls,DihedralOPLS)
#endif
#ifdef DumpInclude
#include "dump_bond.h"
#endif
#ifdef DumpClass
DumpStyle(bond,DumpBond)
#endif
#ifdef FixInclude
#endif
#ifdef FixClass
#endif
#ifdef ImproperInclude
#include "improper_cvff.h"
#include "improper_harmonic.h"
#include "improper_hybrid.h"
#endif
#ifdef ImproperClass
ImproperStyle(cvff,ImproperCvff)
ImproperStyle(harmonic,ImproperHarmonic)
ImproperStyle(hybrid,ImproperHybrid)
#endif
#ifdef PairInclude
#include "pair_lj_charmm_coul_charmm.h"
#include "pair_lj_charmm_coul_charmm_implicit.h"
#endif
#ifdef PairClass
PairStyle(lj/charmm/coul/charmm,PairLJCharmmCoulCharmm)
PairStyle(lj/charmm/coul/charmm/implicit,PairLJCharmmCoulCharmmImplicit)
#endif

30
src/style_opt.h
View File

@ -0,0 +1,30 @@
/* ----------------------------------------------------------------------
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 PairInclude
#include "pair_eam_opt.h"
#include "pair_eam_alloy_opt.h"
#include "pair_eam_fs_opt.h"
#include "pair_lj_charmm_coul_long_opt.h"
#include "pair_lj_cut_opt.h"
#include "pair_morse_opt.h"
#endif
#ifdef PairClass
PairStyle(eam/opt,PairEAMOpt)
PairStyle(eam/alloy/opt,PairEAMAlloyOpt)
PairStyle(eam/fs/opt,PairEAMFSOpt)
PairStyle(lj/cut/opt,PairLJCutOpt)
PairStyle(lj/charmm/coul/long/opt,PairLJCharmmCoulLongOpt)
PairStyle(morse/opt,PairMorseOpt)
#endif

20
src/style_xtc.h
View File

@ -0,0 +1,20 @@
/* ----------------------------------------------------------------------
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 DumpInclude
#include "dump_xtc.h"
#endif
#ifdef DumpClass
DumpStyle(xtc,DumpXTC)
#endif