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

src/integrate.cpp

@@ -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
 ------------------------------------------------------------------------- */

src/integrate.h

@@ -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);
 };

src/kspace.cpp

@@ -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");
   }
 }

src/kspace.h

@@ -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;

src/min.cpp

@@ -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);
   }

src/min.h

@@ -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
 

src/min_fire.cpp

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

src/min_fire.h

@@ -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);

src/min_hftn.cpp

@@ -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];

src/min_hftn.h

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

src/min_linesearch.cpp

@@ -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;

src/min_linesearch.h

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

src/min_quickmin.cpp

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

src/min_quickmin.h

@@ -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);

src/pair.cpp

@@ -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)

src/pair.h

@@ -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
 

src/respa.cpp

@@ -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);
     }

src/verlet.cpp

@@ -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);
     }