Merge release-4-5-patches into release-4-6

[alexxy/gromacs.git] / src / gmxlib / typedefs.c

diff --git a/src/gmxlib/typedefs.c b/src/gmxlib/typedefs.c
index 07ce76e13b61cb5b43b75c948f3ac21240d31c5f..7bec9cd9994809c6b5843a666827d417094330bc 100644 (file)
--- a/src/gmxlib/typedefs.c
+++ b/src/gmxlib/typedefs.c
@@ -44,7 +44,7 @@
 #include "pbc.h"
 #include <string.h>
 
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
 #include "thread_mpi.h"
 #endif
 
@@ -54,20 +54,20 @@
 
 
 static gmx_bool bOverAllocDD=FALSE;
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
 static tMPI_Thread_mutex_t over_alloc_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
 #endif
 
 
 void set_over_alloc_dd(gmx_bool set)
 {
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
     tMPI_Thread_mutex_lock(&over_alloc_mutex);
     /* we just make sure that we don't set this at the same time. 
        We don't worry too much about reading this rarely-set variable */
 #endif    
     bOverAllocDD = set;
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
     tMPI_Thread_mutex_unlock(&over_alloc_mutex);
 #endif    
 }
@@ -193,7 +193,10 @@ void init_top (t_topology *top)
 
 void init_inputrec(t_inputrec *ir)
 {
-  memset(ir,0,(size_t)sizeof(*ir));
+    memset(ir,0,(size_t)sizeof(*ir));
+    snew(ir->fepvals,1);
+    snew(ir->expandedvals,1);
+    snew(ir->simtempvals,1);
 }
 
 void stupid_fill_block(t_block *grp,int natom,gmx_bool bOneIndexGroup)
@@ -423,7 +426,7 @@ void done_inputrec(t_inputrec *ir)
   }
 }
 
-static void init_ekinstate(ekinstate_t *eks)
+static void zero_ekinstate(ekinstate_t *eks)
 {
   eks->ekin_n         = 0;
   eks->ekinh          = NULL;
@@ -493,7 +496,7 @@ void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
         for(i=0; i<state->ngtc; i++)
         {
             for (j=0;j<state->nhchainlength;j++)
- {
+            {
                 state->nosehoover_xi[i*state->nhchainlength + j]  = 0.0;
                 state->nosehoover_vxi[i*state->nhchainlength + j]  = 0.0;
             }
@@ -530,7 +533,7 @@ void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
 }
 
 
-void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength)
+void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda)
 {
   int i;
 
@@ -538,6 +541,11 @@ void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainle
   state->nrng   = 0;
   state->flags  = 0;
   state->lambda = 0;
+  snew(state->lambda,efptNR);
+  for (i=0;i<efptNR;i++)
+  {
+      state->lambda[i] = 0;
+  }
   state->veta   = 0;
   clear_mat(state->box);
   clear_mat(state->box_rel);
@@ -557,10 +565,12 @@ void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainle
   state->sd_X = NULL;
   state->cg_p = NULL;
 
-  init_ekinstate(&state->ekinstate);
+  zero_ekinstate(&state->ekinstate);
 
   init_energyhistory(&state->enerhist);
 
+  init_df_history(&state->dfhist,nlambda,0);
+
   state->ddp_count = 0;
   state->ddp_count_cg_gl = 0;
   state->cg_gl = NULL;
@@ -752,3 +762,70 @@ real max_cutoff(real cutoff1,real cutoff2)
         return max(cutoff1,cutoff2);
     }
 }
+
+extern void init_df_history(df_history_t *dfhist, int nlambda, real wl_delta)
+{
+    int i;
+
+    dfhist->bEquil = 0;
+    dfhist->nlambda = nlambda;
+    dfhist->wl_delta = wl_delta;
+    snew(dfhist->sum_weights,dfhist->nlambda);
+    snew(dfhist->sum_dg,dfhist->nlambda);
+    snew(dfhist->sum_minvar,dfhist->nlambda);
+    snew(dfhist->sum_variance,dfhist->nlambda);
+    snew(dfhist->n_at_lam,dfhist->nlambda);
+    snew(dfhist->wl_histo,dfhist->nlambda);
+
+    /* allocate transition matrices here */
+    snew(dfhist->Tij,dfhist->nlambda);
+    snew(dfhist->Tij_empirical,dfhist->nlambda);
+
+    for (i=0;i<dfhist->nlambda;i++) {
+        snew(dfhist->Tij[i],dfhist->nlambda);
+        snew(dfhist->Tij_empirical[i],dfhist->nlambda);
+    }
+
+    snew(dfhist->accum_p,dfhist->nlambda);
+    snew(dfhist->accum_m,dfhist->nlambda);
+    snew(dfhist->accum_p2,dfhist->nlambda);
+    snew(dfhist->accum_m2,dfhist->nlambda);
+
+    for (i=0;i<dfhist->nlambda;i++) {
+        snew((dfhist->accum_p)[i],dfhist->nlambda);
+        snew((dfhist->accum_m)[i],dfhist->nlambda);
+        snew((dfhist->accum_p2)[i],dfhist->nlambda);
+        snew((dfhist->accum_m2)[i],dfhist->nlambda);
+    }
+}
+
+extern void copy_df_history(df_history_t *df_dest, df_history_t *df_source)
+{
+    int i,j;
+
+    init_df_history(df_dest,df_source->nlambda,df_source->wl_delta);
+    df_dest->nlambda = df_source->nlambda;
+    df_dest->bEquil = df_source->bEquil;
+    for (i=0;i<df_dest->nlambda;i++)
+    {
+        df_dest->sum_weights[i]  = df_source->sum_weights[i];
+        df_dest->sum_dg[i]       = df_source->sum_dg[i];
+        df_dest->sum_minvar[i]   = df_source->sum_minvar[i];
+        df_dest->sum_variance[i] = df_source->sum_variance[i];
+        df_dest->n_at_lam[i]     = df_source->n_at_lam[i];
+        df_dest->wl_histo[i]     = df_source->wl_histo[i];
+        df_dest->accum_p[i]      = df_source->accum_p[i];
+        df_dest->accum_m[i]      = df_source->accum_m[i];
+        df_dest->accum_p2[i]     = df_source->accum_p2[i];
+        df_dest->accum_m2[i]     = df_source->accum_m2[i];
+    }
+
+    for (i=0;i<df_dest->nlambda;i++)
+    {
+        for (j=0;j<df_dest->nlambda;j++)
+        {
+            df_dest->Tij[i][j]  = df_source->Tij[i][j];
+            df_dest->Tij_empirical[i][j]  = df_source->Tij_empirical[i][j];
+        }
+    }
+}