renamed constraint variables rmdr to vir_r_m_dr

Change-Id: Ie332cfdcae3f5b0c0067d8c9a337367395f6065f

diff --git a/include/constr.h b/include/constr.h
index e516ab8ad0c227079d2f9a74017e5e8b6bfa4726..90ebef173e69c2956dcd298c9badc59a3c374f27 100644 (file)
--- a/include/constr.h
+++ b/include/constr.h
@@ -80,8 +80,8 @@ gmx_bool bshakef(FILE *log,           /* Log file                     */
                     real *dvdlambda,    /* FEP force                    */
                     real invdt,         /* 1/delta_t                    */
                     rvec *v,            /* Also constrain v if v!=NULL  */
-                    gmx_bool bCalcVir,      /* Calculate r x m delta_r      */
-                    tensor rmdr,        /* sum r x m delta_r            */
+                    gmx_bool bCalcVir,  /* Calculate r x m delta_r      */
+                    tensor vir_r_m_dr,  /* sum r x m delta_r            */
                     gmx_bool bDumpOnError,  /* Dump debugging stuff on error*/
                     int econq,         /* which type of constrainint is occurring */
                     t_vetavars *vetavar);           /* veta for pressure control */
@@ -107,7 +107,7 @@ void csettle(gmx_settledata_t settled,
              real invdt,         /* 1/delta_t                    */
              real *v,            /* Also constrain v if v!=NULL  */
              int calcvir_atom_end, /* Calculate r x m delta_r up to this atom */
-             tensor rmdr,        /* sum r x m delta_r            */
+             tensor vir_r_m_dr,  /* sum r x m delta_r            */
              int *xerror,
              t_vetavars *vetavar     /* variables for pressure control */   
     );
@@ -118,7 +118,8 @@ void settle_proj(FILE *fp,
                  const t_pbc *pbc,   /* PBC data pointer, can be NULL  */
                  rvec x[],
                  rvec *der,rvec *derp,
-                 int CalcVirAtomEnd,tensor rmdder, t_vetavars *vetavar);
+                 int CalcVirAtomEnd,tensor vir_r_m_dder,
+                 t_vetavars *vetavar);
 /* Analytical algorithm to subtract the components of derivatives
  * of coordinates working on settle type constraint.
  */
@@ -260,7 +261,7 @@ constrain_lincs(FILE *log,gmx_bool bLog,gmx_bool bEner,
                 matrix box,t_pbc *pbc,
                            real lambda,real *dvdlambda,
                            real invdt,rvec *v,
-                           gmx_bool bCalcVir,tensor rmdr,
+                           gmx_bool bCalcVir,tensor vir_r_m_dr,
                            int econ,
                            t_nrnb *nrnb,
                            int maxwarn,int *warncount);

diff --git a/src/mdlib/clincs.c b/src/mdlib/clincs.c
index f4f93362fbc773d81e6fe56bd2af6ff2dcc74e62..46b55b15f7a46a6b001e5aa88d5b3145fee2da2d 100644 (file)
--- a/src/mdlib/clincs.c
+++ b/src/mdlib/clincs.c
@@ -63,7 +63,7 @@ typedef struct {
     int nind_r;       /* number of indices */
     int *ind_r;       /* constraint index for updating atom data */
     int ind_nalloc;   /* allocation size of ind and ind_r */
-    tensor rmdr;      /* temporary variable for virial calculation */
+    tensor vir_r_m_dr;/* temporary variable for virial calculation */
 } lincs_thread_t;
 
 typedef struct gmx_lincsdata {
@@ -466,7 +466,7 @@ static void do_lincs(rvec *x,rvec *xp,matrix box,t_pbc *pbc,
                      gmx_bool bCalcLambda,
                      real wangle,int *warn,
                      real invdt,rvec *v,
-                     gmx_bool bCalcVir,tensor rmdr)
+                     gmx_bool bCalcVir,tensor vir_r_m_dr)
 {
     int     b0,b1,b,i,j,k,n,iter;
     real    tmp0,tmp1,tmp2,im1,im2,mvb,rlen,len,len2,dlen2,wfac;
@@ -680,7 +680,7 @@ static void do_lincs(rvec *x,rvec *xp,matrix box,t_pbc *pbc,
                 tmp1 = tmp0*r[b][i];
                 for(j=0; j<DIM; j++)
                 {
-                    rmdr[i][j] -= tmp1*r[b][j];
+                    vir_r_m_dr[i][j] -= tmp1*r[b][j];
                 }
             }
         } /* 22 ncons flops */
@@ -1432,7 +1432,7 @@ gmx_bool constrain_lincs(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
                          matrix box,t_pbc *pbc,
                          real lambda,real *dvdlambda,
                          real invdt,rvec *v,
-                         gmx_bool bCalcVir,tensor rmdr,
+                         gmx_bool bCalcVir,tensor vir_r_m_dr,
                          int econq,
                          t_nrnb *nrnb,
                          int maxwarn,int *warncount)
@@ -1523,14 +1523,14 @@ gmx_bool constrain_lincs(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
         {
             int th=gmx_omp_get_thread_num();
 
-            clear_mat(lincsd->th[th].rmdr);
+            clear_mat(lincsd->th[th].vir_r_m_dr);
 
             do_lincs(x,xprime,box,pbc,lincsd,th,
                      md->invmass,cr,
                      bCalcVir || (ir->efep != efepNO),
                      ir->LincsWarnAngle,&warn,
                      invdt,v,bCalcVir,
-                     th==0 ? rmdr : lincsd->th[th].rmdr);
+                     th==0 ? vir_r_m_dr : lincsd->th[th].vir_r_m_dr);
         }
 
         if (ir->efep != efepNO)
@@ -1633,7 +1633,7 @@ gmx_bool constrain_lincs(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
 
             do_lincsp(x,xprime,min_proj,pbc,lincsd,th,
                       md->invmass,econq,ir->efep != efepNO ? dvdlambda : NULL,
-                      bCalcVir,th==0 ? rmdr : lincsd->th[th].rmdr);
+                      bCalcVir,th==0 ? vir_r_m_dr : lincsd->th[th].vir_r_m_dr);
         }
     }
 
@@ -1641,7 +1641,7 @@ gmx_bool constrain_lincs(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
     {
         for(i=1; i<lincsd->nth; i++)
         {
-            m_add(rmdr,lincsd->th[i].rmdr,rmdr);
+            m_add(vir_r_m_dr,lincsd->th[i].vir_r_m_dr,vir_r_m_dr);
         }
     }
  

diff --git a/src/mdlib/constr.c b/src/mdlib/constr.c
index f59b3b69960753587587218d36d0a033653dbb1d..d7e0ea958182733eafab8c9cf6322b6dbfbc0e17 100644 (file)
--- a/src/mdlib/constr.c
+++ b/src/mdlib/constr.c
@@ -78,7 +78,7 @@ typedef struct gmx_constr {
   int              warncount_settle;
   gmx_edsam_t      ed;           /* The essential dynamics data        */
 
-    tensor           *rmdr_th;   /* Thread local working data          */
+    tensor           *vir_r_m_dr_th;/* Thread local working data          */
     int              *settle_error; /* Thread local working data          */
 
   gmx_mtop_t       *warn_mtop;   /* Only used for printing warnings    */
@@ -303,7 +303,7 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
     int     start,homenr,nrend;
     int     i,j,d;
     int     ncons,settle_error;
-    tensor  rmdr;
+    tensor  vir_r_m_dr;
     rvec    *vstor;
     real    invdt,vir_fac,t;
     t_ilist *settle;
@@ -348,7 +348,7 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
     
     if (vir != NULL)
     {
-        clear_mat(rmdr);
+        clear_mat(vir_r_m_dr);
     }
     
     where();
@@ -365,9 +365,9 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
         nth = 1;
     }
 
-    if (nth > 1 && constr->rmdr_th == NULL)
+    if (nth > 1 && constr->vir_r_m_dr_th == NULL)
     {
-        snew(constr->rmdr_th,nth);
+        snew(constr->vir_r_m_dr_th,nth);
         snew(constr->settle_error,nth);
     }
     
@@ -409,7 +409,7 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
         bOK = constrain_lincs(fplog,bLog,bEner,ir,step,constr->lincsd,md,cr,
                               x,xprime,min_proj,
                               box,pbc_null,lambda,dvdlambda,
-                              invdt,v,vir!=NULL,rmdr,
+                              invdt,v,vir!=NULL,vir_r_m_dr,
                               econq,nrnb,
                               constr->maxwarn,&constr->warncount_lincs);
         if (!bOK && constr->maxwarn >= 0)
@@ -431,14 +431,16 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
                           homenr,md->invmass,constr->nblocks,constr->sblock,
                           idef,ir,x,xprime,nrnb,
                           constr->lagr,lambda,dvdlambda,
-                          invdt,v,vir!=NULL,rmdr,constr->maxwarn>=0,econq,&vetavar);
+                          invdt,v,vir!=NULL,vir_r_m_dr,
+                          constr->maxwarn>=0,econq,&vetavar);
             break;
         case (econqVeloc):
             bOK = bshakef(fplog,constr->shaked,
                           homenr,md->invmass,constr->nblocks,constr->sblock,
                           idef,ir,x,min_proj,nrnb,
                           constr->lagr,lambda,dvdlambda,
-                          invdt,NULL,vir!=NULL,rmdr,constr->maxwarn>=0,econq,&vetavar);
+                          invdt,NULL,vir!=NULL,vir_r_m_dr,
+                          constr->maxwarn>=0,econq,&vetavar);
             break;
         default:
             gmx_fatal(FARGS,"Internal error, SHAKE called for constraining something else than coordinates");
@@ -479,7 +481,7 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
 
                 if (th > 0)
                 {
-                    clear_mat(constr->rmdr_th[th]);
+                    clear_mat(constr->vir_r_m_dr_th[th]);
                 }
 
                 start_th = (nsettle* th   )/nth;
@@ -492,7 +494,7 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
                             pbc_null,
                             x[0],xprime[0],
                             invdt,v?v[0]:NULL,calcvir_atom_end,
-                            th == 0 ? rmdr : constr->rmdr_th[th],
+                            th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
                             th == 0 ? &settle_error : &constr->settle_error[th],
                             &vetavar);
                 }
@@ -518,7 +520,7 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
 
                 if (th > 0)
                 {
-                    clear_mat(constr->rmdr_th[th]);
+                    clear_mat(constr->vir_r_m_dr_th[th]);
                 }
                 
                 start_th = (nsettle* th   )/nth;
@@ -532,7 +534,7 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
                                 pbc_null,
                                 x,
                                 xprime,min_proj,calcvir_atom_end,
-                                th == 0 ? rmdr : constr->rmdr_th[th],
+                                th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
                                 &vetavar);
                 }
             }
@@ -552,7 +554,7 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
         /* Combine virial and error info of the other threads */
         for(i=1; i<nth; i++)
         {
-            m_add(rmdr,constr->rmdr_th[i],rmdr);
+            m_add(vir_r_m_dr,constr->vir_r_m_dr_th[i],vir_r_m_dr);
             settle_error = constr->settle_error[i];
         } 
 
@@ -610,7 +612,7 @@ gmx_bool constrain(FILE *fplog,gmx_bool bLog,gmx_bool bEner,
         {
             for(j=0; j<DIM; j++)
             {
-                (*vir)[i][j] = vir_fac*rmdr[i][j];
+                (*vir)[i][j] = vir_fac*vir_r_m_dr[i][j];
             }
         }
     }

diff --git a/src/mdlib/csettle.c b/src/mdlib/csettle.c
index e2a2adc2b1bd8c05a4a3b97090dc991126db3f8e..825438c1d7c69304f1b7876d0ddb91dae9e9e8ea 100644 (file)
--- a/src/mdlib/csettle.c
+++ b/src/mdlib/csettle.c
@@ -171,7 +171,8 @@ void settle_proj(FILE *fp,
                  const t_pbc *pbc,
                  rvec x[],
                  rvec *der,rvec *derp,
-                 int calcvir_atom_end,tensor rmdder,t_vetavars *vetavar)
+                 int calcvir_atom_end,tensor vir_r_m_dder,
+                 t_vetavars *vetavar)
 {
     /* Settle for projection out constraint components
      * of derivatives of the coordinates.
@@ -287,7 +288,7 @@ void settle_proj(FILE *fp,
             {
                 for(m2=0; m2<DIM; m2++)
                 {
-                    rmdder[m][m2] +=
+                    vir_r_m_dder[m][m2] +=
                         dOH*roh2[m]*roh2[m2]*fcv[0] +
                         dOH*roh3[m]*roh3[m2]*fcv[1] +
                         dHH*rhh [m]*rhh [m2]*fcv[2]; 
@@ -298,10 +299,10 @@ void settle_proj(FILE *fp,
 
     if (calcvir_atom_end > 0)
     {
-        /* Correct rmdder, which will be used to calcualate the virial;
+        /* Correct r_m_dder, which will be used to calcualate the virial;
          * we need to use the unscaled multipliers in the virial.
          */
-        msmul(rmdder,1.0/vetavar->vscale,rmdder);
+        msmul(vir_r_m_dder,1.0/vetavar->vscale,vir_r_m_dder);
     }
 }
 
@@ -311,7 +312,9 @@ void csettle(gmx_settledata_t settled,
              const t_pbc *pbc,
              real b4[], real after[],
              real invdt,real *v,int CalcVirAtomEnd,
-             tensor rmdr,int *error,t_vetavars *vetavar)
+             tensor vir_r_m_dr,
+             int *error,
+             t_vetavars *vetavar)
 {
     /* ***************************************************************** */
     /*                                                               ** */
@@ -604,15 +607,15 @@ void csettle(gmx_settledata_t settled,
           mdcx = mHs*dcx;
           mdcy = mHs*dcy;
           mdcz = mHs*dcz;
-          rmdr[XX][XX] -= b4[ow1  ]*mdax + (b4[ow1  ]+xb0)*mdbx + (b4[ow1  ]+xc0)*mdcx;
-          rmdr[XX][YY] -= b4[ow1  ]*mday + (b4[ow1  ]+xb0)*mdby + (b4[ow1  ]+xc0)*mdcy;
-          rmdr[XX][ZZ] -= b4[ow1  ]*mdaz + (b4[ow1  ]+xb0)*mdbz + (b4[ow1  ]+xc0)*mdcz;
-          rmdr[YY][XX] -= b4[ow1+1]*mdax + (b4[ow1+1]+yb0)*mdbx + (b4[ow1+1]+yc0)*mdcx;
-          rmdr[YY][YY] -= b4[ow1+1]*mday + (b4[ow1+1]+yb0)*mdby + (b4[ow1+1]+yc0)*mdcy;
-          rmdr[YY][ZZ] -= b4[ow1+1]*mdaz + (b4[ow1+1]+yb0)*mdbz + (b4[ow1+1]+yc0)*mdcz;
-          rmdr[ZZ][XX] -= b4[ow1+2]*mdax + (b4[ow1+2]+zb0)*mdbx + (b4[ow1+2]+zc0)*mdcx;
-          rmdr[ZZ][YY] -= b4[ow1+2]*mday + (b4[ow1+2]+zb0)*mdby + (b4[ow1+2]+zc0)*mdcy;
-          rmdr[ZZ][ZZ] -= b4[ow1+2]*mdaz + (b4[ow1+2]+zb0)*mdbz + (b4[ow1+2]+zc0)*mdcz;
+          vir_r_m_dr[XX][XX] -= b4[ow1  ]*mdax + (b4[ow1  ]+xb0)*mdbx + (b4[ow1  ]+xc0)*mdcx;
+          vir_r_m_dr[XX][YY] -= b4[ow1  ]*mday + (b4[ow1  ]+xb0)*mdby + (b4[ow1  ]+xc0)*mdcy;
+          vir_r_m_dr[XX][ZZ] -= b4[ow1  ]*mdaz + (b4[ow1  ]+xb0)*mdbz + (b4[ow1  ]+xc0)*mdcz;
+          vir_r_m_dr[YY][XX] -= b4[ow1+1]*mdax + (b4[ow1+1]+yb0)*mdbx + (b4[ow1+1]+yc0)*mdcx;
+          vir_r_m_dr[YY][YY] -= b4[ow1+1]*mday + (b4[ow1+1]+yb0)*mdby + (b4[ow1+1]+yc0)*mdcy;
+          vir_r_m_dr[YY][ZZ] -= b4[ow1+1]*mdaz + (b4[ow1+1]+yb0)*mdbz + (b4[ow1+1]+yc0)*mdcz;
+          vir_r_m_dr[ZZ][XX] -= b4[ow1+2]*mdax + (b4[ow1+2]+zb0)*mdbx + (b4[ow1+2]+zc0)*mdcx;
+          vir_r_m_dr[ZZ][YY] -= b4[ow1+2]*mday + (b4[ow1+2]+zb0)*mdby + (b4[ow1+2]+zc0)*mdcy;
+          vir_r_m_dr[ZZ][ZZ] -= b4[ow1+2]*mdaz + (b4[ow1+2]+zb0)*mdbz + (b4[ow1+2]+zc0)*mdcz;
        /* 3*24 - 9 flops */
       }
     } else {

diff --git a/src/mdlib/shakef.c b/src/mdlib/shakef.c
index 10978411241658f07a78485f38b5b0a4dd8d6a21..9adf0a38ce7b8c166582f2b4291bb4d00c796a1f 100644 (file)
--- a/src/mdlib/shakef.c
+++ b/src/mdlib/shakef.c
@@ -179,7 +179,7 @@ int vec_shakef(FILE *fplog,gmx_shakedata_t shaked,
                real tol,rvec x[],rvec prime[],real omega,
                gmx_bool bFEP,real lambda,real lagr[],
                real invdt,rvec *v,
-               gmx_bool bCalcVir,tensor rmdr,int econq, 
+               gmx_bool bCalcVir,tensor vir_r_m_dr,int econq, 
                t_vetavars *vetavar)
 {
     rvec *rij;
@@ -293,7 +293,7 @@ int vec_shakef(FILE *fplog,gmx_shakedata_t shaked,
                 tmp = mm*rij[ll][i];
                 for(j=0; j<DIM; j++) 
                 {
-                    rmdr[i][j] -= tmp*rij[ll][j];
+                    vir_r_m_dr[i][j] -= tmp*rij[ll][j];
                 }
             }
             /* 21 flops */
@@ -358,10 +358,11 @@ static void check_cons(FILE *log,int nc,rvec x[],rvec prime[], rvec v[],
 }
 
 gmx_bool bshakef(FILE *log,gmx_shakedata_t shaked,
-             int natoms,real invmass[],int nblocks,int sblock[],
-             t_idef *idef,t_inputrec *ir,rvec x_s[],rvec prime[],
-             t_nrnb *nrnb,real *lagr,real lambda,real *dvdlambda,
-             real invdt,rvec *v,gmx_bool bCalcVir,tensor rmdr,gmx_bool bDumpOnError,int econq,t_vetavars *vetavar)
+                 int natoms,real invmass[],int nblocks,int sblock[],
+                 t_idef *idef,t_inputrec *ir,rvec x_s[],rvec prime[],
+                 t_nrnb *nrnb,real *lagr,real lambda,real *dvdlambda,
+                 real invdt,rvec *v,gmx_bool bCalcVir,tensor vir_r_m_dr,
+                 gmx_bool bDumpOnError,int econq,t_vetavars *vetavar)
 {
   t_iatom *iatoms;
   real    *lam,dt_2,dvdl;
@@ -384,7 +385,8 @@ gmx_bool bshakef(FILE *log,gmx_shakedata_t shaked,
     blen /= 3;
     n0 = vec_shakef(log,shaked,natoms,invmass,blen,idef->iparams,
                     iatoms,ir->shake_tol,x_s,prime,shaked->omega,
-                    ir->efep!=efepNO,lambda,lam,invdt,v,bCalcVir,rmdr,econq,vetavar);
+                    ir->efep!=efepNO,lambda,lam,invdt,v,bCalcVir,vir_r_m_dr,
+                    econq,vetavar);
 
 #ifdef DEBUGSHAKE
     check_cons(log,blen,x_s,prime,v,idef->iparams,iatoms,invmass,econq);