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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8016 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-04-12 22:32:17 +00:00
parent b82dc33475
commit e4974ae9af
18 changed files with 127 additions and 43 deletions
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15
src/integrate.cpp
View File

@ -14,6 +14,9 @@
#include "stdlib.h"
#include "integrate.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "kspace.h"
#include "modify.h"
#include "compute.h"
@ -38,6 +41,18 @@ Integrate::~Integrate()
delete [] vlist_atom;
}
/* ---------------------------------------------------------------------- */
void Integrate::init()
{
// allow pair and Kspace compute() to be turned off via modify flags
if (force->pair && force->pair->compute_flag) pair_compute_flag = 1;
else pair_compute_flag = 0;
if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1;
else kspace_compute_flag = 0;
}
/* ----------------------------------------------------------------------
setup lists of computes for global and per-atom PE and pressure
------------------------------------------------------------------------- */

5
src/integrate.h
View File

@ -22,7 +22,7 @@ class Integrate : protected Pointers {
public:
Integrate(class LAMMPS *, int, char **);
virtual ~Integrate();
virtual void init() = 0;
virtual void init();
virtual void setup() = 0;
virtual void setup_minimal(int) = 0;
virtual void run(int) = 0;
@ -42,6 +42,9 @@ class Integrate : protected Pointers {
class Compute **vlist_global;
class Compute **vlist_atom;
int pair_compute_flag; // 0 if pair->compute is skipped
int kspace_compute_flag; // 0 if kspace->compute is skipped
void ev_setup();
void ev_set(bigint);
};

18
src/kspace.cpp
View File

@ -28,6 +28,9 @@ using namespace LAMMPS_NS;
KSpace::KSpace(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
{
energy = 0.0;
virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0;
compute_flag = 1;
order = 5;
gridflag = 0;
gewaldflag = 0;
@ -53,6 +56,15 @@ KSpace::~KSpace()
memory->destroy(vatom);
}
/* ---------------------------------------------------------------------- */
void KSpace::compute_dummy(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = evflag_atom = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
@ -149,6 +161,12 @@ void KSpace::modify_params(int narg, char **arg)
error->warning(FLERR,"Kspace_modify slab param < 2.0 may "
"cause unphysical behavior");
slabflag = 1;
} else if (strcmp(arg[iarg],"compute") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) compute_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) compute_flag = 0;
else error->all(FLERR,"Illegal kspace_modify command");
iarg += 2;
} else error->all(FLERR,"Illegal kspace_modify command");
}
}

5
src/kspace.h
View File

@ -29,10 +29,15 @@ class KSpace : protected Pointers {
double g_ewald;
int nx_pppm,ny_pppm,nz_pppm;
int compute_flag; // 0 if skip compute()
KSpace(class LAMMPS *, int, char **);
virtual ~KSpace();
void modify_params(int, char **);
void *extract(const char *);
void compute_dummy(int, int);
// general child-class methods
virtual void init() = 0;
virtual void setup() = 0;

27
src/min.cpp
View File

@ -151,6 +151,13 @@ void Min::init()
rho_flag = 0;
if (atom->rho_flag) rho_flag = 1;
// allow pair and Kspace compute() to be turned off via modify flags
if (force->pair && force->pair->compute_flag) pair_compute_flag = 1;
else pair_compute_flag = 0;
if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1;
else kspace_compute_flag = 0;
// orthogonal vs triclinic simulation box
triclinic = domain->triclinic;
@ -172,10 +179,6 @@ void Min::init()
neighbor->dist_check = 1;
niter = neval = 0;
// style-specific initialization
init_style();
}
/* ----------------------------------------------------------------------
@ -250,7 +253,8 @@ void Min::setup()
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (pair_compute_flag) force->pair->compute(eflag,vflag);
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
@ -261,7 +265,8 @@ void Min::setup()
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
@ -321,7 +326,8 @@ void Min::setup_minimal(int flag)
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (pair_compute_flag) force->pair->compute(eflag,vflag);
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
@ -332,7 +338,8 @@ void Min::setup_minimal(int flag)
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
@ -458,7 +465,7 @@ double Min::energy_force(int resetflag)
timer->stamp();
if (force->pair) {
if (pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(TIME_PAIR);
}
@ -471,7 +478,7 @@ double Min::energy_force(int resetflag)
timer->stamp(TIME_BOND);
}
if (force->kspace) {
if (kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(TIME_KSPACE);
}

5
src/min.h
View File

@ -30,7 +30,7 @@ class Min : protected Pointers {
Min(class LAMMPS *);
virtual ~Min();
void init();
virtual void init();
void setup();
void setup_minimal(int);
void run(int);
@ -66,6 +66,9 @@ class Min : protected Pointers {
int torqueflag,erforceflag;
int e_flag,rho_flag;
int pair_compute_flag; // 0 if pair->compute is skipped
int kspace_compute_flag; // 0 if kspace->compute is skipped
int narray; // # of arrays stored by fix_minimize
class FixMinimize *fix_minimize; // fix that stores auxiliary data

4
src/min_fire.cpp
View File

@ -44,8 +44,10 @@ MinFire::MinFire(LAMMPS *lmp) : Min(lmp) {}
/* ---------------------------------------------------------------------- */
void MinFire::init_style()
void MinFire::init()
{
Min::init();
dt = update->dt;
}

2
src/min_fire.h
View File

@ -28,7 +28,7 @@ class MinFire : public Min {
public:
MinFire(class LAMMPS *);
~MinFire() {}
void init_style();
void init();
void setup_style();
void reset_vectors();
int iterate(int);

6
src/min_hftn.cpp
View File

@ -104,11 +104,13 @@ MinHFTN::~MinHFTN (void)
}
/* ----------------------------------------------------------------------
Public method init_style
Public method init
------------------------------------------------------------------------- */
void MinHFTN::init_style()
void MinHFTN::init()
{
Min::init();
for (int i = 1; i < NUM_HFTN_ATOM_BASED_VECTORS; i++) {
if (_daExtraGlobal[i] != NULL)
delete [] _daExtraGlobal[i];

3
src/min_hftn.h
View File

@ -42,8 +42,7 @@ class MinHFTN : public Min
MinHFTN (LAMMPS *);
~MinHFTN (void);
void init_style();
void init();
void setup_style();
void reset_vectors();
int iterate (int);

4
src/min_linesearch.cpp
View File

@ -77,8 +77,10 @@ MinLineSearch::~MinLineSearch()
/* ---------------------------------------------------------------------- */
void MinLineSearch::init_style()
void MinLineSearch::init()
{
Min::init();
if (linestyle == 0) linemin = &MinLineSearch::linemin_backtrack;
else if (linestyle == 1) linemin = &MinLineSearch::linemin_quadratic;
else if (linestyle == 2) linemin = &MinLineSearch::linemin_forcezero;

2
src/min_linesearch.h
View File

@ -22,7 +22,7 @@ class MinLineSearch : public Min {
public:
MinLineSearch(class LAMMPS *);
~MinLineSearch();
void init_style();
void init();
void setup_style();
void reset_vectors();

4
src/min_quickmin.cpp
View File

@ -41,8 +41,10 @@ MinQuickMin::MinQuickMin(LAMMPS *lmp) : Min(lmp) {}
/* ---------------------------------------------------------------------- */
void MinQuickMin::init_style()
void MinQuickMin::init()
{
Min::init();
dt = update->dt;
}

2
src/min_quickmin.h
View File

@ -28,7 +28,7 @@ class MinQuickMin : public Min {
public:
MinQuickMin(class LAMMPS *);
~MinQuickMin() {}
void init_style();
void init();
void setup_style();
void reset_vectors();
int iterate(int);

15
src/pair.cpp
View File

@ -64,6 +64,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
// pair_modify settings
compute_flag = 1;
offset_flag = 0;
mix_flag = GEOMETRIC;
tail_flag = 0;
@ -127,6 +128,12 @@ void Pair::modify_params(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) tail_flag = 0;
else error->all(FLERR,"Illegal pair_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"compute") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) compute_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) compute_flag = 0;
else error->all(FLERR,"Illegal pair_modify command");
iarg += 2;
} else error->all(FLERR,"Illegal pair_modify command");
}
}
@ -262,6 +269,14 @@ double Pair::mix_distance(double sig1, double sig2)
return value;
}
/* ---------------------------------------------------------------------- */
void Pair::compute_dummy(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)

3
src/pair.h
View File

@ -72,6 +72,8 @@ class Pair : protected Pointers {
class NeighList *listmiddle;
class NeighList *listouter;
int compute_flag; // 0 if skip compute()
Pair(class LAMMPS *);
virtual ~Pair();
@ -84,6 +86,7 @@ class Pair : protected Pointers {
void write_file(int, char **);
void init_bitmap(double, double, int, int &, int &, int &, int &);
virtual void modify_params(int, char **);
void compute_dummy(int, int);
// need to be public, so can be called by pair_style reaxc

32
src/respa.cpp
View File

@ -244,6 +244,8 @@ Respa::~Respa()
void Respa::init()
{
Integrate::init();
// warn if no fixes
if (modify->nfix == 0 && comm->me == 0)
@ -359,17 +361,17 @@ void Respa::setup()
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && force->pair)
if (level_pair == ilevel && pair_compute_flag)
force->pair->compute(eflag,vflag);
if (level_inner == ilevel && force->pair)
if (level_inner == ilevel && pair_compute_flag)
force->pair->compute_inner();
if (level_middle == ilevel && force->pair)
if (level_middle == ilevel && pair_compute_flag)
force->pair->compute_middle();
if (level_outer == ilevel && force->pair)
if (level_outer == ilevel && pair_compute_flag)
force->pair->compute_outer(eflag,vflag);
if (level_kspace == ilevel && force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
}
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
@ -423,17 +425,17 @@ void Respa::setup_minimal(int flag)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && force->pair)
if (level_pair == ilevel && pair_compute_flag)
force->pair->compute(eflag,vflag);
if (level_inner == ilevel && force->pair)
if (level_inner == ilevel && pair_compute_flag)
force->pair->compute_inner();
if (level_middle == ilevel && force->pair)
if (level_middle == ilevel && pair_compute_flag)
force->pair->compute_middle();
if (level_outer == ilevel && force->pair)
if (level_outer == ilevel && pair_compute_flag)
force->pair->compute_outer(eflag,vflag);
if (level_kspace == ilevel && force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
}
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
@ -557,23 +559,23 @@ void Respa::recurse(int ilevel)
force->improper->compute(eflag,vflag);
timer->stamp(TIME_BOND);
}
if (level_pair == ilevel && force->pair) {
if (level_pair == ilevel && pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(TIME_PAIR);
}
if (level_inner == ilevel && force->pair) {
if (level_inner == ilevel && pair_compute_flag) {
force->pair->compute_inner();
timer->stamp(TIME_PAIR);
}
if (level_middle == ilevel && force->pair) {
if (level_middle == ilevel && pair_compute_flag) {
force->pair->compute_middle();
timer->stamp(TIME_PAIR);
}
if (level_outer == ilevel && force->pair) {
if (level_outer == ilevel && pair_compute_flag) {
force->pair->compute_outer(eflag,vflag);
timer->stamp(TIME_PAIR);
}
if (level_kspace == ilevel && force->kspace) {
if (level_kspace == ilevel && kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(TIME_KSPACE);
}

18
src/verlet.cpp
View File

@ -46,6 +46,8 @@ Verlet::Verlet(LAMMPS *lmp, int narg, char **arg) :
void Verlet::init()
{
Integrate::init();
// warn if no fixes
if (modify->nfix == 0 && comm->me == 0)
@ -118,7 +120,8 @@ void Verlet::setup()
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (pair_compute_flag) force->pair->compute(eflag,vflag);
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
@ -129,7 +132,8 @@ void Verlet::setup()
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
@ -172,7 +176,8 @@ void Verlet::setup_minimal(int flag)
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (pair_compute_flag) force->pair->compute(eflag,vflag);
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
@ -183,7 +188,8 @@ void Verlet::setup_minimal(int flag)
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
@ -256,7 +262,7 @@ void Verlet::run(int n)
timer->stamp();
if (force->pair) {
if (pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(TIME_PAIR);
}
@ -269,7 +275,7 @@ void Verlet::run(int n)
timer->stamp(TIME_BOND);
}
if (force->kspace) {
if (kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(TIME_KSPACE);
}