Merge "Fixes inconsistent spelling of Git cmake variables" into release-4-6

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7ba2641292fbfe8e0465de814cb3b6dc14de1b59..1353591a5badfdb5d68fa6cccb102299a15cd28f 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -872,7 +872,6 @@ include(CTest)
 mark_as_advanced(BUILD_TESTING)
 IF(BUILD_TESTING)
        enable_testing()
-       add_test(TestBuildAll make)
        add_subdirectory(tests)
 ENDIF()
 

diff --git a/CTestConfig.cmake b/CTestConfig.cmake
new file mode 100644 (file)
index 0000000..c31b87a
--- /dev/null
+++ b/CTestConfig.cmake
@@ -0,0 +1,13 @@
+SET(CTEST_PROJECT_NAME "Gromacs")
+SET(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
+
+IF(NOT DEFINED CTEST_DROP_METHOD)
+  SET(CTEST_DROP_METHOD "http")
+ENDIF(NOT DEFINED CTEST_DROP_METHOD)
+
+IF(CTEST_DROP_METHOD STREQUAL "http")
+  SET(CTEST_DROP_SITE "cdash.gromacs.org")
+  SET(CTEST_DROP_LOCATION "/submit.php?project=Gromacs")
+  SET(CTEST_DROP_SITE_CDASH TRUE)
+ENDIF(CTEST_DROP_METHOD STREQUAL "http")
+

diff --git a/include/gstat.h b/include/gstat.h
index 574892ec686c4cbb4de4306023760c07301046d7..719fe625125e43794b70da7347e3013086b7c9f0 100644 (file)
--- a/include/gstat.h
+++ b/include/gstat.h
@@ -269,9 +269,9 @@ void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
                              gmx_bool bHisto, const char *fn_histo, int maxchi, 
                              real **dih, int nlist, t_dlist dlist[], 
                               int nframes, int nangles, const char *grpname, 
-                              int xity[], real t0, real dt, gmx_bool bRb, 
+                              int multiplicity[], real t0, real dt, gmx_bool bRb, 
                               real core_frac, const output_env_t oenv); 
-  /* as above but passes dlist so can copy occupancies into it, and xity[] 
+  /* as above but passes dlist so can copy occupancies into it, and multiplicity[] 
    *  (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
    * rotamers. Also production of xvg output files is conditional 
    * and the fractional width of each rotamer can be set ie for a 3 fold 
@@ -402,12 +402,12 @@ int pr_trans(FILE *fp,int nl,t_dlist dl[],real dt,int Xi);
 void mk_chi_lookup (int **lookup, int maxchi, real **dih, 
                           int nlist, t_dlist dlist[]) ; 
 
-void mk_multiplicity_lookup (int *xity, int maxchi, real **dih, 
+void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih, 
                                    int nlist, t_dlist dlist[],int nangle) ; 
 
 void get_chi_product_traj (real **dih,int nframes,int nangles, 
                                  int nlist,int maxchi, t_dlist dlist[], 
-                                  real time[], int **lookup,int *xity,
+                                  real time[], int **lookup,int *multiplicity,
                                   gmx_bool bRb,gmx_bool bNormalize,
                                  real core_frac,gmx_bool bAll,const char *fnall,
                                   const output_env_t oenv); 

diff --git a/include/types/ifunc.h b/include/types/ifunc.h
index 41230b02c3237390e1482074ee3c9a3abc54467e..72026c57c023a1f733e3cef406c89da79438eb2c 100644 (file)
--- a/include/types/ifunc.h
+++ b/include/types/ifunc.h
@@ -105,13 +105,13 @@ typedef struct
 #define NRFP(ftype)  (NRFPA(ftype)+NRFPB(ftype))
 #define NRAL(ftype) (interaction_function[(ftype)].nratoms)
 
-#define IS_CHEMBOND(ftype) (interaction_function[(ftype)].nratoms==2 && interaction_function[(ftype)].flags & IF_CHEMBOND)
+#define IS_CHEMBOND(ftype) (interaction_function[(ftype)].nratoms==2 && (interaction_function[(ftype)].flags & IF_CHEMBOND))
 /* IS_CHEMBOND tells if function type ftype represents a chemical bond */
 
 /* IS_ANGLE tells if a function type ftype represents an angle 
  * Per Larsson, 2007-11-06
  */
-#define IS_ANGLE(ftype) (interaction_function[(ftype)].nratoms==3 && interaction_function[(ftype)].flags & IF_ATYPE)
+#define IS_ANGLE(ftype) (interaction_function[(ftype)].nratoms==3 && (interaction_function[(ftype)].flags & IF_ATYPE))
 #define IS_VSITE(ftype) (interaction_function[(ftype)].flags & IF_VSITE)
 
 #define IS_TABULATED(ftype) (interaction_function[(ftype)].flags & IF_TABULATED)

diff --git a/src/gmxlib/bondfree.c b/src/gmxlib/bondfree.c
index f27df6d4790fb925c4366de6b3c8f1d67894a69f..273804f7010efec7e8c0c56245f693dae4fddbea 100644 (file)
--- a/src/gmxlib/bondfree.c
+++ b/src/gmxlib/bondfree.c
@@ -2611,7 +2611,7 @@ void calc_bonds(FILE *fplog,const gmx_multisim_t *ms,
   /* Loop over all bonded force types to calculate the bonded forces */
   for(ftype=0; (ftype<F_NRE); ftype++) {
          if(ftype<F_GB12 || ftype>F_GB14) {
-    if (interaction_function[ftype].flags & IF_BOND &&
+    if ((interaction_function[ftype].flags & IF_BOND) &&
        !(ftype == F_CONNBONDS || ftype == F_POSRES)) {
       nbonds=idef->il[ftype].nr;
       if (nbonds > 0) {
@@ -2699,7 +2699,7 @@ void calc_bonds_lambda(FILE *fplog,
   for(ftype=0; (ftype<F_NRE); ftype++) {
       if(ftype<F_GB12 || ftype>F_GB14) {
           
-          if (interaction_function[ftype].flags & IF_BOND &&
+          if ((interaction_function[ftype].flags & IF_BOND) &&
               !(ftype == F_CONNBONDS || ftype == F_POSRES)) 
           {
               nbonds_np = idef->il[ftype].nr_nonperturbed;

diff --git a/src/gmxlib/checkpoint.c b/src/gmxlib/checkpoint.c
index b29034741ff81fe655ad6c035a722f1c0b0f8930..41a6a517531ceba57f036ddbfaba2c45b0794464 100644 (file)
--- a/src/gmxlib/checkpoint.c
+++ b/src/gmxlib/checkpoint.c
@@ -1666,7 +1666,7 @@ static void read_checkpoint(const char *fn,FILE **pfplog,
         cp_error();
     }
     *bReadEkin = ((flags_eks & (1<<eeksEKINH)) || (flags_eks & (1<<eeksEKINF)) || (flags_eks & (1<<eeksEKINO)) ||
-                  (flags_eks & (1<<eeksEKINSCALEF)) | (flags_eks & (1<<eeksEKINSCALEH)) | (flags_eks & (1<<eeksVSCALE)));
+                  ((flags_eks & (1<<eeksEKINSCALEF)) | (flags_eks & (1<<eeksEKINSCALEH)) | (flags_eks & (1<<eeksVSCALE))));
     
     ret = do_cpt_enerhist(gmx_fio_getxdr(fp),TRUE,
                           flags_enh,&state->enerhist,NULL);

diff --git a/src/gmxlib/names.c b/src/gmxlib/names.c
index 4f6c1862384062b6a36758deeb3f269e67a49f55..9f9ad810af810eb234eb1c88ef15d42224dd8f2c 100644 (file)
--- a/src/gmxlib/names.c
+++ b/src/gmxlib/names.c
@@ -181,11 +181,11 @@ const char *ewt_names[ewtNR+1] = {
 };
 
 const char *epull_names[epullNR+1] = { 
-  "no", "umbrella", "constraint", "constant_force", NULL
+  "no", "umbrella", "constraint", "constant-force", NULL
 };
 
 const char *epullg_names[epullgNR+1] = { 
-  "distance", "direction", "cylinder", "position", "direction_periodic", NULL
+  "distance", "direction", "cylinder", "position", "direction-periodic", NULL
 };
 
 const char *eQMmethod_names[eQMmethodNR+1] = {

diff --git a/src/gmxlib/selection/sm_insolidangle.c b/src/gmxlib/selection/sm_insolidangle.c
index 1f72fcf1815b40d5a71d681dd5fc80c65042d333..9ed4aaad3e3967e849add22163430483627c484e 100644 (file)
--- a/src/gmxlib/selection/sm_insolidangle.c
+++ b/src/gmxlib/selection/sm_insolidangle.c
@@ -208,9 +208,6 @@ init_data_insolidangle(int npar, gmx_ana_selparam_t *param);
 /** Initializes the \p insolidangle selection method. */
 static int
 init_insolidangle(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
-/** Sets the COM/COG data for the \p insolidangle selection method. */
-static void
-set_comg_insolidangle(gmx_ana_pos_t *pos, void *data);
 /** Frees the data allocated for the \p insolidangle selection method. */
 static void
 free_data_insolidangle(void *data);

diff --git a/src/gmxlib/tcontrol.c b/src/gmxlib/tcontrol.c
index 3c609b90a7966f7ed26cc874cf6906dbd8e9fcbc..f4c2a39e30761ac1ce18b77d965b9f3fd350da65 100644 (file)
--- a/src/gmxlib/tcontrol.c
+++ b/src/gmxlib/tcontrol.c
@@ -63,24 +63,6 @@ static t_timecontrol timecontrol[TNR] = {
 static tMPI_Thread_mutex_t tc_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
 #endif
 
-typedef struct {
-  real tfactor;
-  const char *tstr,*xvgstr;
-} t_timeconvert;
-
-static const t_timeconvert timeconvert[] = {
-    { 0,                   NULL,  NULL       },
-    { 1e3,                "fs",  "fs"       },
-    { 1,                  "ps",  "ps"       },
-    { 1e-3,               "ns",  "ns"       },
-    { 1e-6,               "us",  "\\mus"    }, 
-    { 1e-9,               "ms",  "ms"       },
-    { 1e-12,              "s",   "s"        },
-    { (1.0/60.0)*1e-12,    "m",   "m"        },
-    { (1.0/3600.0)*1e-12,  "h",   "h"        },
-    { 0,                  NULL,  NULL       }
-};
-
 gmx_bool bTimeSet(int tcontrol)
 {
     gmx_bool ret;

diff --git a/src/gmxlib/trxio.c b/src/gmxlib/trxio.c
index 9874339d3e61adfcccf238f1721ea29573d11b68..a4dadff37b461c6447120b3710afa677857bcca3 100644 (file)
--- a/src/gmxlib/trxio.c
+++ b/src/gmxlib/trxio.c
@@ -222,6 +222,7 @@ int write_trxframe_indexed(t_trxstatus *status,t_trxframe *fr,int nind,
       for(i=0; i<nind; i++) 
        copy_rvec(fr->f[ind[i]],fout[i]);
     }
+  /* no break */
   case efXTC:
   case efG87:
     if (fr->bX) {
@@ -277,6 +278,7 @@ int write_trxframe_indexed(t_trxstatus *status,t_trxframe *fr,int nind,
   case efTRR:
     if (vout) sfree(vout);
     if (fout) sfree(fout);
+  /* no break */
   case efXTC:
   case efG87:
     sfree(xout);
@@ -747,13 +749,13 @@ gmx_bool read_next_frame(const output_env_t oenv,t_trxstatus *status,t_trxframe
     }
     
     if (bRet) {
-      bMissingData = ((fr->flags & TRX_NEED_X && !fr->bX) ||
-                     (fr->flags & TRX_NEED_V && !fr->bV) ||
-                     (fr->flags & TRX_NEED_F && !fr->bF));
+      bMissingData = (((fr->flags & TRX_NEED_X) && !fr->bX) ||
+                     ((fr->flags & TRX_NEED_V) && !fr->bV) ||
+                     ((fr->flags & TRX_NEED_F) && !fr->bF));
       bSkip = FALSE;
       if (!bMissingData) {
        ct=check_times2(fr->time,fr->t0,fr->tpf,fr->tppf,fr->bDouble);
-       if (ct == 0 || (fr->flags & TRX_DONT_SKIP && ct<0)) {
+       if (ct == 0 || ((fr->flags & TRX_DONT_SKIP) && ct<0)) {
          printcount(status, oenv,fr->time,FALSE);
        } else if (ct > 0)
          bRet = FALSE;

diff --git a/src/gmxlib/txtdump.c b/src/gmxlib/txtdump.c
index 1314861cacebe010595bf232c374fdccd39e2237..0221e2f36fed35ffbe2f101942971d14d0a1acfc 100644 (file)
--- a/src/gmxlib/txtdump.c
+++ b/src/gmxlib/txtdump.c
@@ -373,13 +373,13 @@ static void pr_grp_opts(FILE *out,int indent,const char *title,t_grpopts *opts,
   fprintf(out,"\n");
   
   pr_indent(out,indent);
-  fprintf(out,"ref_t%s",bMDPformat ? " = " : ":");
+  fprintf(out,"ref-t%s",bMDPformat ? " = " : ":");
   for(i=0; (i<opts->ngtc); i++)
     fprintf(out,"  %10g",opts->ref_t[i]);
   fprintf(out,"\n");
 
   pr_indent(out,indent);
-  fprintf(out,"tau_t%s",bMDPformat ? " = " : ":");
+  fprintf(out,"tau-t%s",bMDPformat ? " = " : ":");
   for(i=0; (i<opts->ngtc); i++)
     fprintf(out,"  %10g",opts->tau_t[i]);
   fprintf(out,"\n");  
@@ -390,7 +390,7 @@ static void pr_grp_opts(FILE *out,int indent,const char *title,t_grpopts *opts,
     fprintf(out,"  %10s",EANNEAL(opts->annealing[i]));
   fprintf(out,"\n");  
  
-  fprintf(out,"ann_npoints%s",bMDPformat ? " = " : ":");
+  fprintf(out,"ann-npoints%s",bMDPformat ? " = " : ":");
   for(i=0; (i<opts->ngtc); i++)
     fprintf(out,"  %10d",opts->anneal_npoints[i]);
   fprintf(out,"\n");  
@@ -425,7 +425,7 @@ static void pr_grp_opts(FILE *out,int indent,const char *title,t_grpopts *opts,
 
   for(i=0; (i<opts->ngener); i++) {
     pr_indent(out,indent);
-    fprintf(out,"energygrp_flags[%3d]:",i);
+    fprintf(out,"energygrp-flags[%3d]:",i);
     for(m=0; (m<opts->ngener); m++)
       fprintf(out," %d",opts->egp_flags[opts->ngener*i+m]);
     fprintf(out,"\n");
@@ -480,7 +480,7 @@ static void pr_cosine(FILE *fp,int indent,const char *title,t_cosines *cos,
 static void pr_pullgrp(FILE *fp,int indent,int g,t_pullgrp *pg)
 {
   pr_indent(fp,indent);
-  fprintf(fp,"pull_group %d:\n",g);
+  fprintf(fp,"pull-group %d:\n",g);
   indent += 2;
   pr_ivec_block(fp,indent,"atom",pg->ind,pg->nat,TRUE);
   pr_rvec(fp,indent,"weight",pg->weight,pg->nweight,TRUE);
@@ -496,14 +496,14 @@ static void pr_pull(FILE *fp,int indent,t_pull *pull)
 {
   int g;
 
-  PS("pull_geometry",EPULLGEOM(pull->eGeom));
-  pr_ivec(fp,indent,"pull_dim",pull->dim,DIM,TRUE);
-  PR("pull_r1",pull->cyl_r1);
-  PR("pull_r0",pull->cyl_r0);
-  PR("pull_constr_tol",pull->constr_tol);
-  PI("pull_nstxout",pull->nstxout);
-  PI("pull_nstfout",pull->nstfout);
-  PI("pull_ngrp",pull->ngrp);
+  PS("pull-geometry",EPULLGEOM(pull->eGeom));
+  pr_ivec(fp,indent,"pull-dim",pull->dim,DIM,TRUE);
+  PR("pull-r1",pull->cyl_r1);
+  PR("pull-r0",pull->cyl_r0);
+  PR("pull-constr-tol",pull->constr_tol);
+  PI("pull-nstxout",pull->nstxout);
+  PI("pull-nstfout",pull->nstfout);
+  PI("pull-ngrp",pull->ngrp);
   for(g=0; g<pull->ngrp+1; g++)
     pr_pullgrp(fp,indent,g,&pull->grp[g]);
 }
@@ -519,12 +519,12 @@ void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
       indent=pr_title(fp,indent,title);
     PS("integrator",EI(ir->eI));
     PSTEP("nsteps",ir->nsteps);
-    PSTEP("init_step",ir->init_step);
-    PS("ns_type",ENS(ir->ns_type));
+    PSTEP("init-step",ir->init_step);
+    PS("ns-type",ENS(ir->ns_type));
     PI("nstlist",ir->nstlist);
     PI("ndelta",ir->ndelta);
     PI("nstcomm",ir->nstcomm);
-    PS("comm_mode",ECOM(ir->comm_mode));
+    PS("comm-mode",ECOM(ir->comm_mode));
     PI("nstlog",ir->nstlog);
     PI("nstxout",ir->nstxout);
     PI("nstvout",ir->nstvout);
@@ -532,18 +532,18 @@ void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
     PI("nstcalcenergy",ir->nstcalcenergy);
     PI("nstenergy",ir->nstenergy);
     PI("nstxtcout",ir->nstxtcout);
-    PR("init_t",ir->init_t);
-    PR("delta_t",ir->delta_t);
+    PR("init-t",ir->init_t);
+    PR("delta-t",ir->delta_t);
     
     PR("xtcprec",ir->xtcprec);
     PI("nkx",ir->nkx);
     PI("nky",ir->nky);
     PI("nkz",ir->nkz);
-    PI("pme_order",ir->pme_order);
-    PR("ewald_rtol",ir->ewald_rtol);
-    PR("ewald_geometry",ir->ewald_geometry);
-    PR("epsilon_surface",ir->epsilon_surface);
-    PS("optimize_fft",BOOL(ir->bOptFFT));
+    PI("pme-order",ir->pme_order);
+    PR("ewald-rtol",ir->ewald_rtol);
+    PR("ewald-geometry",ir->ewald_geometry);
+    PR("epsilon-surface",ir->epsilon_surface);
+    PS("optimize-fft",BOOL(ir->bOptFFT));
     PS("ePBC",EPBC(ir->ePBC));
     PS("bPeriodicMols",BOOL(ir->bPeriodicMols));
     PS("bContinuation",BOOL(ir->bContinuation));
@@ -553,119 +553,119 @@ void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
     PS("epc",EPCOUPLTYPE(ir->epc));
     PS("epctype",EPCOUPLTYPETYPE(ir->epct));
     PI("nstpcouple",ir->nstpcouple);
-    PR("tau_p",ir->tau_p);
-    pr_matrix(fp,indent,"ref_p",ir->ref_p,bMDPformat);
+    PR("tau-p",ir->tau_p);
+    pr_matrix(fp,indent,"ref-p",ir->ref_p,bMDPformat);
     pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
-    PS("refcoord_scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
+    PS("refcoord-scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
     if (bMDPformat)
-      fprintf(fp,"posres_com  = %g %g %g\n",ir->posres_com[XX],
+      fprintf(fp,"posres-com  = %g %g %g\n",ir->posres_com[XX],
              ir->posres_com[YY],ir->posres_com[ZZ]);
     else
-      pr_rvec(fp,indent,"posres_com",ir->posres_com,DIM,TRUE);
+      pr_rvec(fp,indent,"posres-com",ir->posres_com,DIM,TRUE);
     if (bMDPformat)
-      fprintf(fp,"posres_comB = %g %g %g\n",ir->posres_comB[XX],
+      fprintf(fp,"posres-comB = %g %g %g\n",ir->posres_comB[XX],
              ir->posres_comB[YY],ir->posres_comB[ZZ]);
     else
-      pr_rvec(fp,indent,"posres_comB",ir->posres_comB,DIM,TRUE);
-    PI("andersen_seed",ir->andersen_seed);
+      pr_rvec(fp,indent,"posres-comB",ir->posres_comB,DIM,TRUE);
+    PI("andersen-seed",ir->andersen_seed);
     PR("rlist",ir->rlist);
     PR("rlistlong",ir->rlistlong);
     PR("rtpi",ir->rtpi);
     PS("coulombtype",EELTYPE(ir->coulombtype));
-    PR("rcoulomb_switch",ir->rcoulomb_switch);
+    PR("rcoulomb-switch",ir->rcoulomb_switch);
     PR("rcoulomb",ir->rcoulomb);
     PS("vdwtype",EVDWTYPE(ir->vdwtype));
-    PR("rvdw_switch",ir->rvdw_switch);
+    PR("rvdw-switch",ir->rvdw_switch);
     PR("rvdw",ir->rvdw);
     if (ir->epsilon_r != 0)
-      PR("epsilon_r",ir->epsilon_r);
+      PR("epsilon-r",ir->epsilon_r);
     else
-      PS("epsilon_r",infbuf);
+      PS("epsilon-r",infbuf);
     if (ir->epsilon_rf != 0)
-      PR("epsilon_rf",ir->epsilon_rf);
+      PR("epsilon-rf",ir->epsilon_rf);
     else
-      PS("epsilon_rf",infbuf);
+      PS("epsilon-rf",infbuf);
     PR("tabext",ir->tabext);
-    PS("implicit_solvent",EIMPLICITSOL(ir->implicit_solvent));
-    PS("gb_algorithm",EGBALGORITHM(ir->gb_algorithm));
-    PR("gb_epsilon_solvent",ir->gb_epsilon_solvent);
+    PS("implicit-solvent",EIMPLICITSOL(ir->implicit_solvent));
+    PS("gb-algorithm",EGBALGORITHM(ir->gb_algorithm));
+    PR("gb-epsilon-solvent",ir->gb_epsilon_solvent);
     PI("nstgbradii",ir->nstgbradii);
     PR("rgbradii",ir->rgbradii);
-    PR("gb_saltconc",ir->gb_saltconc);
-    PR("gb_obc_alpha",ir->gb_obc_alpha);
-    PR("gb_obc_beta",ir->gb_obc_beta);
-    PR("gb_obc_gamma",ir->gb_obc_gamma);
-    PR("gb_dielectric_offset",ir->gb_dielectric_offset);
-    PS("sa_algorithm",ESAALGORITHM(ir->gb_algorithm));
-    PR("sa_surface_tension",ir->sa_surface_tension);
+    PR("gb-saltconc",ir->gb_saltconc);
+    PR("gb-obc-alpha",ir->gb_obc_alpha);
+    PR("gb-obc-beta",ir->gb_obc_beta);
+    PR("gb-obc-gamma",ir->gb_obc_gamma);
+    PR("gb-dielectric-offset",ir->gb_dielectric_offset);
+    PS("sa-algorithm",ESAALGORITHM(ir->gb_algorithm));
+    PR("sa-surface-tension",ir->sa_surface_tension);
          
     PS("DispCorr",EDISPCORR(ir->eDispCorr));
-    PS("free_energy",EFEPTYPE(ir->efep));
-    PR("init_lambda",ir->init_lambda);
-    PR("delta_lambda",ir->delta_lambda);
+    PS("free-energy",EFEPTYPE(ir->efep));
+    PR("init-lambda",ir->init_lambda);
+    PR("delta-lambda",ir->delta_lambda);
     if (!bMDPformat)
     {
-        PI("n_foreign_lambda",ir->n_flambda);
+        PI("n-foreign-lambda",ir->n_flambda);
     }
     if (ir->n_flambda > 0)
     {
         pr_indent(fp,indent);
-        fprintf(fp,"foreign_lambda%s",bMDPformat ? " = " : ":");
+        fprintf(fp,"foreign-lambda%s",bMDPformat ? " = " : ":");
         for(i=0; i<ir->n_flambda; i++)
         {
             fprintf(fp,"  %10g",ir->flambda[i]);
         }
         fprintf(fp,"\n");
     }
-    PR("sc_alpha",ir->sc_alpha);
-    PI("sc_power",ir->sc_power);
-    PR("sc_sigma",ir->sc_sigma);
-    PR("sc_sigma_min",ir->sc_sigma_min);
+    PR("sc-alpha",ir->sc_alpha);
+    PI("sc-power",ir->sc_power);
+    PR("sc-sigma",ir->sc_sigma);
+    PR("sc-sigma-min",ir->sc_sigma_min);
     PI("nstdhdl", ir->nstdhdl);
-    PS("separate_dhdl_file", SEPDHDLFILETYPE(ir->separate_dhdl_file));
-    PS("dhdl_derivatives", DHDLDERIVATIVESTYPE(ir->dhdl_derivatives));
-    PI("dh_hist_size", ir->dh_hist_size);
-    PD("dh_hist_spacing", ir->dh_hist_spacing);
+    PS("separate-dhdl-file", SEPDHDLFILETYPE(ir->separate_dhdl_file));
+    PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(ir->dhdl_derivatives));
+    PI("dh-hist-size", ir->dh_hist_size);
+    PD("dh-hist-spacing", ir->dh_hist_spacing);
 
     PI("nwall",ir->nwall);
-    PS("wall_type",EWALLTYPE(ir->wall_type));
-    PI("wall_atomtype[0]",ir->wall_atomtype[0]);
-    PI("wall_atomtype[1]",ir->wall_atomtype[1]);
-    PR("wall_density[0]",ir->wall_density[0]);
-    PR("wall_density[1]",ir->wall_density[1]);
-    PR("wall_ewald_zfac",ir->wall_ewald_zfac);
+    PS("wall-type",EWALLTYPE(ir->wall_type));
+    PI("wall-atomtype[0]",ir->wall_atomtype[0]);
+    PI("wall-atomtype[1]",ir->wall_atomtype[1]);
+    PR("wall-density[0]",ir->wall_density[0]);
+    PR("wall-density[1]",ir->wall_density[1]);
+    PR("wall-ewald-zfac",ir->wall_ewald_zfac);
 
     PS("pull",EPULLTYPE(ir->ePull));
     if (ir->ePull != epullNO)
       pr_pull(fp,indent,ir->pull);
 
     PS("disre",EDISRETYPE(ir->eDisre));
-    PS("disre_weighting",EDISREWEIGHTING(ir->eDisreWeighting));
-    PS("disre_mixed",BOOL(ir->bDisreMixed));
-    PR("dr_fc",ir->dr_fc);
-    PR("dr_tau",ir->dr_tau);
+    PS("disre-weighting",EDISREWEIGHTING(ir->eDisreWeighting));
+    PS("disre-mixed",BOOL(ir->bDisreMixed));
+    PR("dr-fc",ir->dr_fc);
+    PR("dr-tau",ir->dr_tau);
     PR("nstdisreout",ir->nstdisreout);
-    PR("orires_fc",ir->orires_fc);
-    PR("orires_tau",ir->orires_tau);
+    PR("orires-fc",ir->orires_fc);
+    PR("orires-tau",ir->orires_tau);
     PR("nstorireout",ir->nstorireout);
 
     PR("dihre-fc",ir->dihre_fc);
     
-    PR("em_stepsize",ir->em_stepsize);
-    PR("em_tol",ir->em_tol);
+    PR("em-stepsize",ir->em_stepsize);
+    PR("em-tol",ir->em_tol);
     PI("niter",ir->niter);
-    PR("fc_stepsize",ir->fc_stepsize);
+    PR("fc-stepsize",ir->fc_stepsize);
     PI("nstcgsteep",ir->nstcgsteep);
     PI("nbfgscorr",ir->nbfgscorr);
 
     PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
-    PR("shake_tol",ir->shake_tol);
-    PI("lincs_order",ir->nProjOrder);
-    PR("lincs_warnangle",ir->LincsWarnAngle);
-    PI("lincs_iter",ir->nLincsIter);
-    PR("bd_fric",ir->bd_fric);
-    PI("ld_seed",ir->ld_seed);
-    PR("cos_accel",ir->cos_accel);
+    PR("shake-tol",ir->shake_tol);
+    PI("lincs-order",ir->nProjOrder);
+    PR("lincs-warnangle",ir->LincsWarnAngle);
+    PI("lincs-iter",ir->nLincsIter);
+    PR("bd-fric",ir->bd_fric);
+    PI("ld-seed",ir->ld_seed);
+    PR("cos-accel",ir->cos_accel);
     pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
     PI("userint1",ir->userint1);
     PI("userint2",ir->userint2);
@@ -686,7 +686,7 @@ void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
     PI("QMconstraints",ir->QMconstraints);
     PI("QMMMscheme",ir->QMMMscheme);
     PR("scalefactor",ir->scalefactor);
-    pr_qm_opts(fp,indent,"qm_opts",&(ir->opts));
+    pr_qm_opts(fp,indent,"qm-opts",&(ir->opts));
   }
 }
 #undef PS

diff --git a/src/gmxlib/wman.c b/src/gmxlib/wman.c
index 4b42bb11ee87bd2eb6c5b289b6753522f68d3de4..4c51f10a80cdea832bc640db35d9bccac44394be 100644 (file)
--- a/src/gmxlib/wman.c
+++ b/src/gmxlib/wman.c
@@ -1025,6 +1025,7 @@ static void write_py(FILE *out,const char *program,
       for(j=2; (pa[i].u.c[j] != NULL); j++)
        fprintf(out,",'%s'",pa[i].u.c[j]);
       fprintf(out,"],%d))\n",is_hidden(&(pa[i])));
+      break;
     default:
       break;
     }

diff --git a/src/kernel/readir.c b/src/kernel/readir.c
index aad2f4cdfe62151f8fb1fa733de2878246fa2e82..50f6a8a75307e4831bd24242e4c3f4775cea673f 100644 (file)
--- a/src/kernel/readir.c
+++ b/src/kernel/readir.c
@@ -414,12 +414,12 @@ void check_ir(const char *mdparin,t_inputrec *ir, t_gromppopts *opts,
     {
         dt_pcoupl = ir->nstpcouple*ir->delta_t;
 
-        sprintf(err_buf,"tau_p must be > 0 instead of %g\n",ir->tau_p);
+        sprintf(err_buf,"tau-p must be > 0 instead of %g\n",ir->tau_p);
         CHECK(ir->tau_p <= 0);
         
         if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
         {
-            sprintf(warn_buf,"For proper integration of the %s barostat, tau_p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
+            sprintf(warn_buf,"For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
                     EPCOUPLTYPE(ir->epc),ir->tau_p,pcouple_min_integration_steps(ir->epc),dt_pcoupl);
             warning(wi,warn_buf);
         }      
@@ -467,19 +467,19 @@ void check_ir(const char *mdparin,t_inputrec *ir, t_gromppopts *opts,
   }
 
   if (ir->epsilon_r!=1 && ir->implicit_solvent==eisGBSA) {
-    sprintf(warn_buf,"epsilon_r = %g with GB implicit solvent, will use this value for inner dielectric",ir->epsilon_r);
+    sprintf(warn_buf,"epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric",ir->epsilon_r);
     warning_note(wi,warn_buf);
   }
 
   if (EEL_RF(ir->coulombtype) && ir->epsilon_rf==1 && ir->epsilon_r!=1) {
-    sprintf(warn_buf,"epsilon_r = %g and epsilon_rf = 1 with reaction field, assuming old format and exchanging epsilon_r and epsilon_rf",ir->epsilon_r);
+    sprintf(warn_buf,"epsilon-r = %g and epsilon-rf = 1 with reaction field, assuming old format and exchanging epsilon-r and epsilon-rf",ir->epsilon_r);
     warning(wi,warn_buf);
     ir->epsilon_rf = ir->epsilon_r;
     ir->epsilon_r  = 1.0;
   }
 
   if (getenv("GALACTIC_DYNAMICS") == NULL) {  
-    sprintf(err_buf,"epsilon_r must be >= 0 instead of %g\n",ir->epsilon_r);
+    sprintf(err_buf,"epsilon-r must be >= 0 instead of %g\n",ir->epsilon_r);
     CHECK(ir->epsilon_r < 0);
   }
   
@@ -487,16 +487,16 @@ void check_ir(const char *mdparin,t_inputrec *ir, t_gromppopts *opts,
     /* reaction field (at the cut-off) */
     
     if (ir->coulombtype == eelRF_ZERO) {
-       sprintf(err_buf,"With coulombtype = %s, epsilon_rf must be 0",
+       sprintf(err_buf,"With coulombtype = %s, epsilon-rf must be 0",
               eel_names[ir->coulombtype]);
       CHECK(ir->epsilon_rf != 0);
     }
 
-    sprintf(err_buf,"epsilon_rf must be >= epsilon_r");
+    sprintf(err_buf,"epsilon-rf must be >= epsilon-r");
     CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
          (ir->epsilon_r == 0));
     if (ir->epsilon_rf == ir->epsilon_r) {
-      sprintf(warn_buf,"Using epsilon_rf = epsilon_r with %s does not make sense",
+      sprintf(warn_buf,"Using epsilon-rf = epsilon-r with %s does not make sense",
              eel_names[ir->coulombtype]);
       warning(wi,warn_buf);
     }
@@ -541,23 +541,23 @@ void check_ir(const char *mdparin,t_inputrec *ir, t_gromppopts *opts,
 
   if (EEL_PME(ir->coulombtype)) {
     if (ir->pme_order < 3) {
-        warning_error(wi,"pme_order can not be smaller than 3");
+        warning_error(wi,"pme-order can not be smaller than 3");
     }
   }
 
   if (ir->nwall==2 && EEL_FULL(ir->coulombtype)) {
     if (ir->ewald_geometry == eewg3D) {
-      sprintf(warn_buf,"With pbc=%s you should use ewald_geometry=%s",
+      sprintf(warn_buf,"With pbc=%s you should use ewald-geometry=%s",
              epbc_names[ir->ePBC],eewg_names[eewg3DC]);
       warning(wi,warn_buf);
     }
     /* This check avoids extra pbc coding for exclusion corrections */
-    sprintf(err_buf,"wall_ewald_zfac should be >= 2");
+    sprintf(err_buf,"wall-ewald-zfac should be >= 2");
     CHECK(ir->wall_ewald_zfac < 2);
   }
 
   if (EVDW_SWITCHED(ir->vdwtype)) {
-    sprintf(err_buf,"With vdwtype = %s rvdw_switch must be < rvdw",
+    sprintf(err_buf,"With vdwtype = %s rvdw-switch must be < rvdw",
            evdw_names[ir->vdwtype]);
     CHECK(ir->rvdw_switch >= ir->rvdw);
   } else if (ir->vdwtype == evdwCUT) {
@@ -634,7 +634,7 @@ void check_ir(const char *mdparin,t_inputrec *ir, t_gromppopts *opts,
     ir->implicit_solvent=eisGBSA;
     fprintf(stderr,"Note: Old option for generalized born electrostatics given:\n"
            "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
-           "setting implicit_solvent value to \"GBSA\" in input section.\n");
+            "setting implicit-solvent value to \"GBSA\" in input section.\n");
   }
 
   if(ir->sa_algorithm==esaSTILL)
@@ -767,14 +767,14 @@ static void do_wall_params(t_inputrec *ir,
             nstr = str_nelem(wall_density,MAXPTR,names);
             if (nstr != ir->nwall)
             {
-                gmx_fatal(FARGS,"Expected %d elements for wall_density, found %d",ir->nwall,nstr);
+                gmx_fatal(FARGS,"Expected %d elements for wall-density, found %d",ir->nwall,nstr);
             }
             for(i=0; i<ir->nwall; i++)
             {
                 sscanf(names[i],"%lf",&dbl);
                 if (dbl <= 0)
                 {
-                    gmx_fatal(FARGS,"wall_density[%d] = %f\n",i,dbl);
+                    gmx_fatal(FARGS,"wall-density[%d] = %f\n",i,dbl);
                 }
                 ir->wall_density[i] = dbl;
             }
@@ -838,9 +838,9 @@ void get_ir(const char *mdparin,const char *mdparout,
   RTYPE ("dt",         ir->delta_t,    0.001);
   STEPTYPE ("nsteps",   ir->nsteps,     0);
   CTYPE ("For exact run continuation or redoing part of a run");
-  STEPTYPE ("init_step",ir->init_step,  0);
+  STEPTYPE ("init-step",ir->init_step,  0);
   CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
-  ITYPE ("simulation_part", ir->simulation_part, 1);
+  ITYPE ("simulation-part", ir->simulation_part, 1);
   CTYPE ("mode for center of mass motion removal");
   EETYPE("comm-mode",   ir->comm_mode,  ecm_names);
   CTYPE ("number of steps for center of mass motion removal");
@@ -858,7 +858,7 @@ void get_ir(const char *mdparin,const char *mdparout,
   CTYPE ("Force tolerance and initial step-size");
   RTYPE ("emtol",       ir->em_tol,     10.0);
   RTYPE ("emstep",      ir->em_stepsize,0.01);
-  CTYPE ("Max number of iterations in relax_shells");
+  CTYPE ("Max number of iterations in relax-shells");
   ITYPE ("niter",       ir->niter,      20);
   CTYPE ("Step size (ps^2) for minimization of flexible constraints");
   RTYPE ("fcstep",      ir->fc_stepsize, 0);
@@ -899,7 +899,7 @@ void get_ir(const char *mdparin,const char *mdparout,
   ir->ndelta = 2;
   CTYPE ("Periodic boundary conditions: xyz, no, xy");
   EETYPE("pbc",         ir->ePBC,       epbc_names);
-  EETYPE("periodic_molecules", ir->bPeriodicMols, yesno_names);
+  EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
   CTYPE ("nblist cut-off");
   RTYPE ("rlist",      ir->rlist,      1.0);
   CTYPE ("long-range cut-off for switched potentials");
@@ -913,8 +913,8 @@ void get_ir(const char *mdparin,const char *mdparout,
   RTYPE ("rcoulomb-switch",    ir->rcoulomb_switch,    0.0);
   RTYPE ("rcoulomb",   ir->rcoulomb,   1.0);
   CTYPE ("Relative dielectric constant for the medium and the reaction field");
-  RTYPE ("epsilon_r",   ir->epsilon_r,  1.0);
-  RTYPE ("epsilon_rf",  ir->epsilon_rf, 1.0);
+  RTYPE ("epsilon-r",   ir->epsilon_r,  1.0);
+  RTYPE ("epsilon-rf",  ir->epsilon_rf, 1.0);
   CTYPE ("Method for doing Van der Waals");
   EETYPE("vdw-type",   ir->vdwtype,    evdw_names);
   CTYPE ("cut-off lengths");
@@ -925,44 +925,44 @@ void get_ir(const char *mdparin,const char *mdparout,
   CTYPE ("Extension of the potential lookup tables beyond the cut-off");
   RTYPE ("table-extension", ir->tabext, 1.0);
   CTYPE ("Seperate tables between energy group pairs");
-  STYPE ("energygrp_table", egptable,   NULL);
+  STYPE ("energygrp-table", egptable,   NULL);
   CTYPE ("Spacing for the PME/PPPM FFT grid");
   RTYPE ("fourierspacing", opts->fourierspacing,0.12);
   CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
-  ITYPE ("fourier_nx",  ir->nkx,         0);
-  ITYPE ("fourier_ny",  ir->nky,         0);
-  ITYPE ("fourier_nz",  ir->nkz,         0);
+  ITYPE ("fourier-nx",  ir->nkx,         0);
+  ITYPE ("fourier-ny",  ir->nky,         0);
+  ITYPE ("fourier-nz",  ir->nkz,         0);
   CTYPE ("EWALD/PME/PPPM parameters");
-  ITYPE ("pme_order",   ir->pme_order,   4);
-  RTYPE ("ewald_rtol",  ir->ewald_rtol, 0.00001);
-  EETYPE("ewald_geometry", ir->ewald_geometry, eewg_names);
-  RTYPE ("epsilon_surface", ir->epsilon_surface, 0.0);
-  EETYPE("optimize_fft",ir->bOptFFT,  yesno_names);
+  ITYPE ("pme-order",   ir->pme_order,   4);
+  RTYPE ("ewald-rtol",  ir->ewald_rtol, 0.00001);
+  EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
+  RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
+  EETYPE("optimize-fft",ir->bOptFFT,  yesno_names);
 
   CCTYPE("IMPLICIT SOLVENT ALGORITHM");
-  EETYPE("implicit_solvent", ir->implicit_solvent, eis_names);
+  EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
        
   CCTYPE ("GENERALIZED BORN ELECTROSTATICS"); 
   CTYPE ("Algorithm for calculating Born radii");
-  EETYPE("gb_algorithm", ir->gb_algorithm, egb_names);
+  EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
   CTYPE ("Frequency of calculating the Born radii inside rlist");
   ITYPE ("nstgbradii", ir->nstgbradii, 1);
   CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
   CTYPE ("between rlist and rgbradii is updated every nstlist steps");
   RTYPE ("rgbradii",  ir->rgbradii, 1.0);
   CTYPE ("Dielectric coefficient of the implicit solvent");
-  RTYPE ("gb_epsilon_solvent",ir->gb_epsilon_solvent, 80.0);   
+  RTYPE ("gb-epsilon-solvent",ir->gb_epsilon_solvent, 80.0);
   CTYPE ("Salt concentration in M for Generalized Born models");
-  RTYPE ("gb_saltconc",  ir->gb_saltconc, 0.0); 
+  RTYPE ("gb-saltconc",  ir->gb_saltconc, 0.0);
   CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
-  RTYPE ("gb_obc_alpha", ir->gb_obc_alpha, 1.0);
-  RTYPE ("gb_obc_beta", ir->gb_obc_beta, 0.8);
-  RTYPE ("gb_obc_gamma", ir->gb_obc_gamma, 4.85);      
-  RTYPE ("gb_dielectric_offset", ir->gb_dielectric_offset, 0.009);
-  EETYPE("sa_algorithm", ir->sa_algorithm, esa_names);
+  RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
+  RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
+  RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
+  RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
+  EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
   CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
   CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
-  RTYPE ("sa_surface_tension", ir->sa_surface_tension, -1);
+  RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
                 
   /* Coupling stuff */
   CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
@@ -975,19 +975,19 @@ void get_ir(const char *mdparin,const char *mdparout,
   CTYPE ("Time constant (ps) and reference temperature (K)");
   STYPE ("tau-t",      tau_t,          NULL);
   STYPE ("ref-t",      ref_t,          NULL);
-  CTYPE ("Pressure coupling");
-  EETYPE("Pcoupl",     ir->epc,        epcoupl_names);
-  EETYPE("Pcoupltype", ir->epct,       epcoupltype_names);
+  CTYPE ("pressure coupling");
+  EETYPE("pcoupl",     ir->epc,        epcoupl_names);
+  EETYPE("pcoupltype", ir->epct,       epcoupltype_names);
   ITYPE ("nstpcouple", ir->nstpcouple,  -1);
   CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
   RTYPE ("tau-p",      ir->tau_p,      1.0);
   STYPE ("compressibility",    dumstr[0],      NULL);
   STYPE ("ref-p",       dumstr[1],      NULL);
   CTYPE ("Scaling of reference coordinates, No, All or COM");
-  EETYPE ("refcoord_scaling",ir->refcoord_scaling,erefscaling_names);
+  EETYPE ("refcoord-scaling",ir->refcoord_scaling,erefscaling_names);
 
   CTYPE ("Random seed for Andersen thermostat");
-  ITYPE ("andersen_seed", ir->andersen_seed, 815131);
+  ITYPE ("andersen-seed", ir->andersen_seed, 815131);
 
   /* QMMM */
   CCTYPE ("OPTIONS FOR QMMM calculations");
@@ -1023,11 +1023,11 @@ void get_ir(const char *mdparin,const char *mdparout,
   CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
   STYPE ("annealing",   anneal,      NULL);
   CTYPE ("Number of time points to use for specifying annealing in each group");
-  STYPE ("annealing_npoints", anneal_npoints, NULL);
+  STYPE ("annealing-npoints", anneal_npoints, NULL);
   CTYPE ("List of times at the annealing points for each group");
-  STYPE ("annealing_time",       anneal_time,       NULL);
+  STYPE ("annealing-time",       anneal_time,       NULL);
   CTYPE ("Temp. at each annealing point, for each group.");
-  STYPE ("annealing_temp",  anneal_temp,  NULL);
+  STYPE ("annealing-temp",  anneal_temp,  NULL);
   
   /* Startup run */
   CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
@@ -1061,21 +1061,21 @@ void get_ir(const char *mdparin,const char *mdparout,
   /* Energy group exclusions */
   CCTYPE ("ENERGY GROUP EXCLUSIONS");
   CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
-  STYPE ("energygrp_excl", egpexcl,     NULL);
+  STYPE ("energygrp-excl", egpexcl,     NULL);
   
   /* Walls */
   CCTYPE ("WALLS");
   CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
   ITYPE ("nwall", ir->nwall, 0);
-  EETYPE("wall_type",     ir->wall_type,   ewt_names);
-  RTYPE ("wall_r_linpot", ir->wall_r_linpot, -1);
-  STYPE ("wall_atomtype", wall_atomtype, NULL);
-  STYPE ("wall_density",  wall_density,  NULL);
-  RTYPE ("wall_ewald_zfac", ir->wall_ewald_zfac, 3);
+  EETYPE("wall-type",     ir->wall_type,   ewt_names);
+  RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
+  STYPE ("wall-atomtype", wall_atomtype, NULL);
+  STYPE ("wall-density",  wall_density,  NULL);
+  RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
   
   /* COM pulling */
   CCTYPE("COM PULLING");
-  CTYPE("Pull type: no, umbrella, constraint or constant_force");
+  CTYPE("Pull type: no, umbrella, constraint or constant-force");
   EETYPE("pull",          ir->ePull, epull_names);
   if (ir->ePull != epullNO) {
     snew(ir->pull,1);
@@ -1111,7 +1111,7 @@ void get_ir(const char *mdparin,const char *mdparout,
   EETYPE("free-energy",        ir->efep, efep_names);
   RTYPE ("init-lambda",        ir->init_lambda,0.0);
   RTYPE ("delta-lambda",ir->delta_lambda,0.0);
-  STYPE ("foreign_lambda", foreign_lambda, NULL);
+  STYPE ("foreign-lambda", foreign_lambda, NULL);
   RTYPE ("sc-alpha",ir->sc_alpha,0.0);
   ITYPE ("sc-power",ir->sc_power,0);
   RTYPE ("sc-sigma",ir->sc_sigma,0.3);
@@ -1119,8 +1119,8 @@ void get_ir(const char *mdparin,const char *mdparout,
   EETYPE("separate-dhdl-file", ir->separate_dhdl_file, 
                                separate_dhdl_file_names);
   EETYPE("dhdl-derivatives", ir->dhdl_derivatives, dhdl_derivatives_names);
-  ITYPE ("dh_hist_size", ir->dh_hist_size, 0);
-  RTYPE ("dh_hist_spacing", ir->dh_hist_spacing, 0.1);
+  ITYPE ("dh-hist-size", ir->dh_hist_size, 0);
+  RTYPE ("dh-hist-spacing", ir->dh_hist_spacing, 0.1);
   STYPE ("couple-moltype",  couple_moltype,  NULL);
   EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
   EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
@@ -1238,7 +1238,7 @@ void get_ir(const char *mdparin,const char *mdparout,
        warning(wi,"For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
       }
     } else {
-      warning(wi,"Can not couple a molecule with free_energy = no");
+      warning(wi,"Can not couple a molecule with free-energy = no");
     }
   }
 
@@ -1820,8 +1820,8 @@ void do_index(const char* mdparin, const char *ndx,
   nref_t = str_nelem(ref_t,MAXPTR,ptr2);
   ntcg   = str_nelem(tcgrps,MAXPTR,ptr3);
   if ((ntau_t != ntcg) || (nref_t != ntcg)) {
-    gmx_fatal(FARGS,"Invalid T coupling input: %d groups, %d ref_t values and "
-               "%d tau_t values",ntcg,nref_t,ntau_t);
+    gmx_fatal(FARGS,"Invalid T coupling input: %d groups, %d ref-t values and "
+                "%d tau-t values",ntcg,nref_t,ntau_t);
   }
 
   bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI==eiBD || EI_TPI(ir->eI));
@@ -1833,14 +1833,14 @@ void do_index(const char* mdparin, const char *ndx,
   snew(ir->opts.tau_t,nr);
   snew(ir->opts.ref_t,nr);
   if (ir->eI==eiBD && ir->bd_fric==0) {
-    fprintf(stderr,"bd_fric=0, so tau_t will be used as the inverse friction constant(s)\n"); 
+    fprintf(stderr,"bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
   }
 
   if (bSetTCpar)
   {
       if (nr != nref_t)
       {
-          gmx_fatal(FARGS,"Not enough ref_t and tau_t values!");
+          gmx_fatal(FARGS,"Not enough ref-t and tau-t values!");
       }
       
       tau_min = 1e20;
@@ -1849,7 +1849,7 @@ void do_index(const char* mdparin, const char *ndx,
           ir->opts.tau_t[i] = strtod(ptr1[i],NULL);
           if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
           {
-              sprintf(warn_buf,"With integrator %s tau_t should be larger than 0",ei_names[ir->eI]);
+              sprintf(warn_buf,"With integrator %s tau-t should be larger than 0",ei_names[ir->eI]);
               warning_error(wi,warn_buf);
           }
           if ((ir->etc == etcVRESCALE && ir->opts.tau_t[i] >= 0) || 
@@ -1882,7 +1882,7 @@ void do_index(const char* mdparin, const char *ndx,
       {
           if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
           {
-              sprintf(warn_buf,"For proper integration of the %s thermostat, tau_t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
+              sprintf(warn_buf,"For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
                       ETCOUPLTYPE(ir->etc),
                       tau_min,nstcmin,
                       ir->nsttcouple*ir->delta_t);
@@ -1894,7 +1894,7 @@ void do_index(const char* mdparin, const char *ndx,
           ir->opts.ref_t[i] = strtod(ptr2[i],NULL);
           if (ir->opts.ref_t[i] < 0)
           {
-              gmx_fatal(FARGS,"ref_t for group %d negative",i);
+              gmx_fatal(FARGS,"ref-t for group %d negative",i);
           }
       }
   }
@@ -1933,7 +1933,7 @@ void do_index(const char* mdparin, const char *ndx,
        /* Read the other fields too */
        nSA_points = str_nelem(anneal_npoints,MAXPTR,ptr1);
        if(nSA_points!=nSA) 
-         gmx_fatal(FARGS,"Found %d annealing_npoints values for %d groups\n",nSA_points,nSA);
+          gmx_fatal(FARGS,"Found %d annealing-npoints values for %d groups\n",nSA_points,nSA);
        for(k=0,i=0;i<nr;i++) {
          ir->opts.anneal_npoints[i]=strtol(ptr1[i],NULL,10);
          if(ir->opts.anneal_npoints[i]==1)
@@ -1945,10 +1945,10 @@ void do_index(const char* mdparin, const char *ndx,
 
        nSA_time = str_nelem(anneal_time,MAXPTR,ptr1);
        if(nSA_time!=k) 
-         gmx_fatal(FARGS,"Found %d annealing_time values, wanter %d\n",nSA_time,k);
+          gmx_fatal(FARGS,"Found %d annealing-time values, wanter %d\n",nSA_time,k);
        nSA_temp = str_nelem(anneal_temp,MAXPTR,ptr2);
        if(nSA_temp!=k) 
-         gmx_fatal(FARGS,"Found %d annealing_temp values, wanted %d\n",nSA_temp,k);
+          gmx_fatal(FARGS,"Found %d annealing-temp values, wanted %d\n",nSA_temp,k);
 
        for(i=0,k=0;i<nr;i++) {
          
@@ -2171,11 +2171,11 @@ void do_index(const char* mdparin, const char *ndx,
   nr = groups->grps[egcENER].nr;
   snew(ir->opts.egp_flags,nr*nr);
 
-  bExcl = do_egp_flag(ir,groups,"energygrp_excl",egpexcl,EGP_EXCL);
+  bExcl = do_egp_flag(ir,groups,"energygrp-excl",egpexcl,EGP_EXCL);
   if (bExcl && EEL_FULL(ir->coulombtype))
     warning(wi,"Can not exclude the lattice Coulomb energy between energy groups");
 
-  bTable = do_egp_flag(ir,groups,"energygrp_table",egptable,EGP_TABLE);
+  bTable = do_egp_flag(ir,groups,"energygrp-table",egptable,EGP_TABLE);
   if (bTable && !(ir->vdwtype == evdwUSER) && 
       !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
       !(ir->coulombtype == eelPMEUSERSWITCH))
@@ -2368,7 +2368,7 @@ void triple_check(const char *mdparin,t_inputrec *ir,gmx_mtop_t *sys,
     for(i=0; (i<ir->opts.ngtc); i++)
       gdt_max = max(gdt_max,ir->delta_t/ir->opts.tau_t[i]);
     if (0.5*gdt_max > 0.0015) {
-      sprintf(warn_buf,"The relative error with integrator %s is 0.5*delta_t/tau_t = %g, you might want to switch to integrator %s\n",
+      sprintf(warn_buf,"The relative error with integrator %s is 0.5*delta-t/tau-t = %g, you might want to switch to integrator %s\n",
              ei_names[ir->eI],0.5*gdt_max,ei_names[eiSD2]);
       warning_note(wi,warn_buf);
     }
@@ -2460,7 +2460,7 @@ void double_check(t_inputrec *ir,matrix box,gmx_bool bConstr,warninp_t wi)
 
   if (bConstr && ir->eConstrAlg == econtSHAKE) {
     if (ir->shake_tol <= 0.0) {
-      sprintf(warn_buf,"ERROR: shake_tol must be > 0 instead of %g\n",
+      sprintf(warn_buf,"ERROR: shake-tol must be > 0 instead of %g\n",
               ir->shake_tol);
       warning_error(wi,warn_buf);
     }
@@ -2484,7 +2484,7 @@ void double_check(t_inputrec *ir,matrix box,gmx_bool bConstr,warninp_t wi)
     }
     
     if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder<8)) {
-      sprintf(warn_buf,"For accurate %s with LINCS constraints, lincs_order should be 8 or more.",ei_names[ir->eI]);
+      sprintf(warn_buf,"For accurate %s with LINCS constraints, lincs-order should be 8 or more.",ei_names[ir->eI]);
       warning_note(wi,warn_buf);
     }
     if (ir->epc==epcMTTK) {

diff --git a/src/kernel/topdirs.c b/src/kernel/topdirs.c
index b5c3c0a1fb37e84ffa9275041ed26c4fefa6285a..14dd59fc00a7388bf45795a81912836e442d6509 100644 (file)
--- a/src/kernel/topdirs.c
+++ b/src/kernel/topdirs.c
@@ -76,6 +76,7 @@ int ifunc_index(directive d,int type)
       gmx_fatal(FARGS,"Invalid bond type %d",type);
       break;
     }
+    break;
   case d_angles:
   case d_angletypes:
     switch (type) {
@@ -97,7 +98,8 @@ int ifunc_index(directive d,int type)
       gmx_fatal(FARGS,"Invalid angle type %d",type);
       break;
     }
-    case d_pairs:
+    break;
+  case d_pairs:
   case d_pairtypes:
     if (type == 1 || (d == d_pairtypes && type == 2))
       return F_LJ14;
@@ -105,6 +107,7 @@ int ifunc_index(directive d,int type)
       return F_LJC14_Q;
     else
       gmx_fatal(FARGS,"Invalid pairs type %d",type);
+    break;
   case d_pairs_nb:
     return F_LJC_PAIRS_NB;
   case d_dihedrals:
@@ -152,6 +155,7 @@ int ifunc_index(directive d,int type)
     default:
       gmx_fatal(FARGS,"Invalid vsites3 type %d",type);
     }
+    break;
   case d_vsites4:
       switch (type) {
           case 1:
@@ -161,6 +165,7 @@ int ifunc_index(directive d,int type)
           default:
               gmx_fatal(FARGS,"Invalid vsites4 type %d",type);
       }
+      break;
   case d_vsitesn:
     return F_VSITEN; 
   case d_constraints:
@@ -173,6 +178,7 @@ int ifunc_index(directive d,int type)
     default:
       gmx_fatal(FARGS,"Invalid constraints type %d",type);
     }
+    break;
   case d_settles:
     return F_SETTLE;
   case d_position_restraints:
@@ -181,9 +187,11 @@ int ifunc_index(directive d,int type)
       return F_POSRES;
     case 2:
       gmx_fatal(FARGS,"Water polarization should now be listed under [ water_polarization ]\n");
+      break;
     default:
       gmx_fatal(FARGS,"Invalid position restraint type %d",type);
     }
+    break;
   case d_polarization:
     return F_POLARIZATION;
   case d_thole_polarization:

diff --git a/src/mdlib/domdec.c b/src/mdlib/domdec.c
index 2bae6564136acc54860a52c3e5bcae0ca01241ad..ecf3ac3c95f08ebed2402249fc634935785f71dc 100644 (file)
--- a/src/mdlib/domdec.c
+++ b/src/mdlib/domdec.c
@@ -1481,7 +1481,7 @@ void dd_collect_state(gmx_domdec_t *dd,
     }
     for(est=0; est<estNR; est++)
     {
-        if (EST_DISTR(est) && state_local->flags & (1<<est))
+        if (EST_DISTR(est) && (state_local->flags & (1<<est)))
         {
             switch (est) {
             case estX:
@@ -1563,7 +1563,7 @@ static void dd_realloc_state(t_state *state,rvec **f,int nalloc)
     
     for(est=0; est<estNR; est++)
     {
-        if (EST_DISTR(est) && state->flags & (1<<est))
+        if (EST_DISTR(est) && (state->flags & (1<<est)))
         {
             switch(est) {
             case estX:
@@ -1756,7 +1756,7 @@ static void dd_distribute_state(gmx_domdec_t *dd,t_block *cgs,
     }
     for(i=0; i<estNR; i++)
     {
-        if (EST_DISTR(i) && state_local->flags & (1<<i))
+        if (EST_DISTR(i) && (state_local->flags & (1<<i)))
         {
             switch (i) {
             case estX:
@@ -4132,7 +4132,7 @@ static void rotate_state_atom(t_state *state,int a)
 
     for(est=0; est<estNR; est++)
     {
-        if (EST_DISTR(est) && state->flags & (1<<est)) {
+        if (EST_DISTR(est) && (state->flags & (1<<est))) {
             switch (est) {
             case estX:
                 /* Rotate the complete state; for a rectangular box only */
@@ -7993,7 +7993,7 @@ static void dd_sort_state(gmx_domdec_t *dd,int ePBC,
     /* Reorder the state */
     for(i=0; i<estNR; i++)
     {
-        if (EST_DISTR(i) && state->flags & (1<<i))
+        if (EST_DISTR(i) && (state->flags & (1<<i)))
         {
             switch (i)
             {

diff --git a/src/mdlib/edsam.c b/src/mdlib/edsam.c
index f4e770aca4343c26682ff277af8ec0b17194c167..8359863d3b2081edc924c8c267fe3b0b61a3ba36 100644 (file)
--- a/src/mdlib/edsam.c
+++ b/src/mdlib/edsam.c
@@ -1497,9 +1497,7 @@ static int read_edi(FILE* in, gmx_edsam_t ed,t_edpar *edi,int nr_mdatoms, int ed
     {
         if (readmagic==666 || readmagic==667 || readmagic==668)
             gmx_fatal(FARGS,"Wrong magic number: Use newest version of make_edi to produce edi file");
-        else if (readmagic == 669)
-            ;
-        else
+        else if (readmagic != 669)
             gmx_fatal(FARGS,"Wrong magic number %d in %s",readmagic,ed->edinam);
     }
 

diff --git a/src/mdlib/fft5d.c b/src/mdlib/fft5d.c
index dbbcdaf4e053e177836f8c1b45735abaf2909f95..e2f5266ec423b9eeb791f11034034274a3031be8 100644 (file)
--- a/src/mdlib/fft5d.c
+++ b/src/mdlib/fft5d.c
@@ -101,6 +101,7 @@ static int lfactor(int z) {
        int i;
        for (i=sqrt(z);;i--)
                if (z%i==0) return i;
+       return 1;
 }
 
 /* largest factor */
@@ -109,6 +110,7 @@ static int l2factor(int z) {
        if (z==1) return 1;
        for (i=z/2;;i--)
                if (z%i==0) return i;
+       return 1;
 }
 
 /* largest prime factor: WARNING: slow recursion, only use for small numbers */
@@ -795,7 +797,7 @@ static void compute_offsets(fft5d_plan plan, int xs[], int xl[], int xc[], int N
             rotate(NG);            
         }
     }
-    if (plan->flags&FFT5D_REALCOMPLEX && ((!(plan->flags&FFT5D_BACKWARD) && s==0) || (plan->flags&FFT5D_BACKWARD && s==2))) {
+    if ((plan->flags&FFT5D_REALCOMPLEX) && ((!(plan->flags&FFT5D_BACKWARD) && s==0) || ((plan->flags&FFT5D_BACKWARD) && s==2))) {
         xl[0] = rC[s];
     }
 }
@@ -1033,7 +1035,7 @@ void fft5d_compare_data(const t_complex* lin, const t_complex* in, fft5d_plan pl
     int x,y,z,l;
     int *coor = plan->coor;
     int ll=2; /*compare ll values per element (has to be 2 for complex)*/
-    if (plan->flags&FFT5D_REALCOMPLEX && plan->flags&FFT5D_BACKWARD) 
+    if ((plan->flags&FFT5D_REALCOMPLEX) && (plan->flags&FFT5D_BACKWARD))
     {
         ll=1;
     }

diff --git a/src/mdlib/wall.c b/src/mdlib/wall.c
index 168d56a532d677e23800db06d6e673fc5024ec71..beb4d7cf5c34483e11bb6c93af59c9c12cef3c9d 100644 (file)
--- a/src/mdlib/wall.c
+++ b/src/mdlib/wall.c
@@ -169,7 +169,7 @@ real do_walls(t_inputrec *ir,t_forcerec *fr,matrix box,t_mdatoms *md,
                 at = type[i];
                 Cd = nbfp[ntw[w]+2*at];
                 Cr = nbfp[ntw[w]+2*at+1];
-                if (!((Cd==0 && Cr==0) || egp_flags[ggid] & EGP_EXCL))
+                if (!((Cd==0 && Cr==0) || (egp_flags[ggid] & EGP_EXCL)))
                 {
                     if (w == 0)
                     {

diff --git a/src/ngmx/nener.c b/src/ngmx/nener.c
index 42b7d0d306e3fb6382ca289dfcfa006b0bda53f9..b21c72695b4a4337c7f0830038323520b54f45e3 100644 (file)
--- a/src/ngmx/nener.c
+++ b/src/ngmx/nener.c
@@ -125,7 +125,7 @@ static gmx_bool EWCallBack(t_x11 *x11,XEvent *event, Window w, void *data)
   case ClientMessage:
     ew->etype=event->xclient.data.l[0];
     ExposeWin(x11->disp,ew->wd.self);
-    /* Fall thru... */
+    /* no break */
   case ButtonRelease:
     hide_menu(x11,ew->selener);
     break;

diff --git a/src/ngmx/ngmx.c b/src/ngmx/ngmx.c
index 5c399573129135acffbd65f7f6b4a1d8e04d107f..a3ce8e14b9843b587b2c935c4594fd3129ac4631 100644 (file)
--- a/src/ngmx/ngmx.c
+++ b/src/ngmx/ngmx.c
@@ -60,8 +60,6 @@
 void init_gmx(t_x11 *x11,char *program,int nfile,t_filenm fnm[],
               const output_env_t oenv);
 
-int EventSignaller(t_manager *man);
-
 static void dump_xw(char *dispname,Window w,char *fn)
 {
   char comm[256];

diff --git a/src/tools/acf.test.c b/src/tools/acf.test.c
index 6bde6ce9ee54a382b5f3d4618423c00b606c760c..5babfe2aabd60bf05f3d09c383762511b38440b5 100644 (file)
--- a/src/tools/acf.test.c
+++ b/src/tools/acf.test.c
@@ -106,9 +106,10 @@ int main(int argc,char *argv[])
       break;
     case 5:
       if (i==0)
-       data[i] = 1;
+        data[i] = 1;
       else
-       data[i] = sin(x)/(x);
+        data[i] = sin(x)/(x);
+      break;
     default:
       /* Data remains 0.0 */
       break;

diff --git a/src/tools/anadih.c b/src/tools/anadih.c
index 91a67c102c53b13de22d7fcb581ff35edacfea43..c3c32dbaff19ae14d63ec0afab02f1a0563e1cdd 100644 (file)
--- a/src/tools/anadih.c
+++ b/src/tools/anadih.c
@@ -119,28 +119,28 @@ void ana_dih_trans(const char *fn_trans,const char *fn_histo,
   /* just a wrapper; declare extra args, then chuck away at end. */ 
   int maxchi = 0 ; 
   t_dlist *dlist ; 
-  int *xity; 
+  int *multiplicity; 
   int nlist = nangles ; 
   int k ; 
 
   snew(dlist,nlist);  
-  snew(xity,nangles); 
+  snew(multiplicity,nangles); 
   for(k=0; (k<nangles); k++) {
-    xity[k]=3 ; 
+    multiplicity[k]=3 ; 
   }
 
   low_ana_dih_trans(TRUE, fn_trans,TRUE, fn_histo, maxchi, 
                     dih, nlist, dlist, nframes,
-                   nangles, grpname, xity, t0, dt, bRb, 0.5,oenv); 
+                   nangles, grpname, multiplicity, t0, dt, bRb, 0.5,oenv); 
   sfree(dlist); 
-  sfree(xity); 
+  sfree(multiplicity); 
   
 }
 
 void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
                       gmx_bool bHisto, const char *fn_histo, int maxchi, 
                       real **dih, int nlist, t_dlist dlist[], int nframes,
-                      int nangles, const char *grpname, int xity[], 
+                      int nangles, const char *grpname, int multiplicity[], 
                       real t0, real dt, gmx_bool bRb, real core_frac,
                        const output_env_t oenv)
 {
@@ -178,12 +178,12 @@ void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
 #ifdef OLDIE
     mind = maxd = prev = dih[i][0]; 
 #else
-    cur_bin = calc_bin(dih[i][0],xity[i],core_frac);
+    cur_bin = calc_bin(dih[i][0],multiplicity[i],core_frac);
     rot_occ[cur_bin][i]++ ; 
 #endif    
     for (j=1; (j<nframes); j++)
     {
-      new_bin = calc_bin(dih[i][j],xity[i],core_frac);
+      new_bin = calc_bin(dih[i][j],multiplicity[i],core_frac);
       rot_occ[new_bin][i]++ ; 
 #ifndef OLDIE
       if (cur_bin == 0)
@@ -281,11 +281,11 @@ void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
 
 }
 
-void mk_multiplicity_lookup (int *xity, int maxchi, real **dih, 
+void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih, 
                             int nlist, t_dlist dlist[],int nangles) 
 {
   /* new by grs - for dihedral j (as in dih[j]) get multiplicity from dlist
-   * and store in xity[j] 
+   * and store in multiplicity[j] 
    */ 
 
   int j, Dih, i ; 
@@ -300,11 +300,11 @@ void mk_multiplicity_lookup (int *xity, int maxchi, real **dih,
          ((Dih == edOmega) && (has_dihedral(edOmega,&(dlist[i])))) ||
          ((Dih  > edOmega) && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1))) {
        /* default - we will correct the rest below */ 
-       xity[j] = 3 ; 
+       multiplicity[j] = 3 ; 
 
        /* make omegas 2fold, though doesn't make much more sense than 3 */ 
        if (Dih == edOmega && (has_dihedral(edOmega,&(dlist[i])))) {
-         xity[j] = 2 ; 
+         multiplicity[j] = 2 ; 
        } 
 
        /* dihedrals to aromatic rings, COO, CONH2 or guanidinium are 2fold*/
@@ -319,7 +319,7 @@ void mk_multiplicity_lookup (int *xity, int maxchi, real **dih,
               ((strstr(name,"GLN") != NULL) && (Dih == edChi3))  ||   
               ((strstr(name,"ASN") != NULL) && (Dih == edChi2))  ||   
               ((strstr(name,"ARG") != NULL) && (Dih == edChi4))  ) {
-           xity[j] = 2; 
+           multiplicity[j] = 2; 
          }
        }
        j++ ; 
@@ -331,7 +331,7 @@ void mk_multiplicity_lookup (int *xity, int maxchi, real **dih,
            j,nangles);
   /* Check for remaining dihedrals */
   for(;(j < nangles); j++)
-    xity[j] = 3;
+    multiplicity[j] = 3;
 
 }
 
@@ -369,7 +369,7 @@ void mk_chi_lookup (int **lookup, int maxchi, real **dih,
 
 void get_chi_product_traj (real **dih,int nframes,int nangles, int nlist,
                           int maxchi, t_dlist dlist[], real time[], 
-                          int **lookup, int *xity,gmx_bool bRb, gmx_bool bNormalize,
+                          int **lookup, int *multiplicity,gmx_bool bRb, gmx_bool bNormalize,
                           real core_frac, gmx_bool bAll, const char *fnall,
                            const output_env_t oenv) 
 {
@@ -407,7 +407,7 @@ void get_chi_product_traj (real **dih,int nframes,int nangles, int nlist,
     for (Xi = 0 ; Xi < maxchi ; Xi ++ ) {
       index = lookup[i][Xi] ; /* chi_(Xi+1) of res i (-1 if off end) */ 
       if ( index >= 0 ) {
-       n = xity[index]; 
+       n = multiplicity[index]; 
        nbin = n*nbin ; 
       }
     }
@@ -423,14 +423,14 @@ void get_chi_product_traj (real **dih,int nframes,int nangles, int nlist,
        bRotZero = TRUE ; 
        bHaveChi = FALSE ; 
       } else {
-       b = calc_bin(dih[index][j],xity[index],core_frac) ; 
+       b = calc_bin(dih[index][j],multiplicity[index],core_frac) ; 
        accum = b - 1 ; 
        if (b == 0 ) 
          bRotZero = TRUE ; 
        for (Xi = 1 ; Xi < maxchi ; Xi ++ ) {
          index = lookup[i][Xi] ; /* chi_(Xi+1) of res i (-1 if off end) */ 
          if ( index >= 0 ) {
-           n = xity[index]; 
+           n = multiplicity[index]; 
            b = calc_bin(dih[index][j],n,core_frac); 
            accum = n * accum + b - 1 ; 
            if (b == 0 ) 

diff --git a/src/tools/expfit.c b/src/tools/expfit.c
index 7ea7566b18809394dee4edda6d5cc287524e4e31..c16144ddb9903c47027d9b1ba58d20378c2ea443 100644 (file)
--- a/src/tools/expfit.c
+++ b/src/tools/expfit.c
@@ -69,12 +69,6 @@ const char *longs_ffn[effnNR] = {
   "y = a2*ee(a1,x) + (1-a2)*ee(a2,x)"
 };
 
-extern gmx_bool mrqmin(real x[],real y[],real sig[],int ndata,real a[],
-                  int ma,int lista[],int mfit,real **covar,real **alpha,
-                  real *chisq,
-                  void (*funcs)(real x,real a[],real *y,real dyda[]),
-                  real *alamda);
-
 extern gmx_bool mrqmin_new(real x[],real y[],real sig[],int ndata,real a[], 
                       int ia[],int ma,real **covar,real **alpha,real *chisq, 
                       void (*funcs)(real, real [], real *, real []), 

diff --git a/src/tools/gmx_chi.c b/src/tools/gmx_chi.c
index c3971e575ebb4c9928fe16dd1ad0b67f76eef506..94db178b6b71ba096df2def57e8b4baedccd8b13 100644 (file)
--- a/src/tools/gmx_chi.c
+++ b/src/tools/gmx_chi.c
@@ -1133,7 +1133,7 @@ int gmx_chi(int argc,char *argv[])
   atom_id    isize,*index;
   int        ndih,nactdih,nf;
   real       **dih,*trans_frac,*aver_angle,*time;
-  int        i,j,**chi_lookup,*xity; 
+  int        i,j,**chi_lookup,*multiplicity; 
   
   t_filenm  fnm[] = {
     { efSTX, "-s",  NULL,     ffREAD  },
@@ -1252,8 +1252,8 @@ int gmx_chi(int argc,char *argv[])
    *
    * added multiplicity */ 
 
-  snew(xity,ndih) ;
-  mk_multiplicity_lookup(xity, maxchi, dih, nlist, dlist,ndih); 
+  snew(multiplicity,ndih) ;
+  mk_multiplicity_lookup(multiplicity, maxchi, dih, nlist, dlist,ndih); 
  
   strcpy(grpname, "All residues, "); 
   if(bPhi) 
@@ -1270,7 +1270,7 @@ int gmx_chi(int argc,char *argv[])
 
   low_ana_dih_trans(bDo_ot, opt2fn("-ot",NFILE,fnm),
                    bDo_oh, opt2fn("-oh",NFILE,fnm),maxchi, 
-                   dih, nlist, dlist, nf, nactdih, grpname, xity, 
+                   dih, nlist, dlist, nf, nactdih, grpname, multiplicity, 
                    *time,  dt, FALSE, core_frac,oenv) ; 
 
   /* Order parameters */  
@@ -1303,7 +1303,7 @@ int gmx_chi(int argc,char *argv[])
     mk_chi_lookup(chi_lookup, maxchi, dih, nlist, dlist); 
     
     get_chi_product_traj(dih,nf,nactdih,nlist,
-                        maxchi,dlist,time,chi_lookup,xity,
+                        maxchi,dlist,time,chi_lookup,multiplicity,
                         FALSE,bNormHisto, core_frac,bAll,
                         opt2fn("-cp",NFILE,fnm),oenv); 
 

diff --git a/src/tools/gmx_editconf.c b/src/tools/gmx_editconf.c
index 3662585b71abc74a999c76e3d5e2581d1f37abb1..7d33eb4a251442bd3068a21697e0e9a4d0363a2b 100644 (file)
--- a/src/tools/gmx_editconf.c
+++ b/src/tools/gmx_editconf.c
@@ -79,8 +79,6 @@ typedef struct
     int nsatm;
     t_simat sat[3];
 } t_simlist;
-static const char *pdbtp[epdbNR] =
-    { "ATOM  ", "HETATM" };
 
 real calc_mass(t_atoms *atoms, gmx_bool bGetMass, gmx_atomprop_t aps)
 {

diff --git a/src/tools/gmx_enemat.c b/src/tools/gmx_enemat.c
index 480e4ded1c97073aae828c0b8efde4bc2b11c8e4..48b6bd7497c0ba3748e3bedd16ab34e6a81fd404 100644 (file)
--- a/src/tools/gmx_enemat.c
+++ b/src/tools/gmx_enemat.c
@@ -352,8 +352,6 @@ int gmx_enemat(int argc,char *argv[])
     }
    
     emid = 0.0;/*(emin+emax)*0.5;*/
-    for(m=0; (m<egNR); m++)
-      egrp_nm[m]=egrp_nm[m];
     egrp_nm[egTotal]="total";
     for (m=0; (m<egNR+egSP); m++) 
       if (egrp_use[m]) {

diff --git a/src/tools/make_edi.c b/src/tools/make_edi.c
index 409fb4764c9d9819e7dae4addb8aac640b68d481..22694d0f2a900e912ce717243306a97d613ced3e 100644 (file)
--- a/src/tools/make_edi.c
+++ b/src/tools/make_edi.c
@@ -235,14 +235,15 @@ int sscan_list(int *list[], const char *str, const char *listname) {
 
        /* format error occured */
        case sError:
-       gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d with char %c",listname,pos-startpos,*(pos-1));
-
+          gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d with char %c",listname,pos-startpos,*(pos-1));
+          break;
        /* logical error occured */
        case sZero:
-               gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d: eigenvector 0 is not valid",listname,pos-startpos);
+                  gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d: eigenvector 0 is not valid",listname,pos-startpos);
+                  break;
        case sSmaller:
-               gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d: second index %d is not bigger than %d",listname,pos-startpos,end_number,number);
-
+                  gmx_fatal(FARGS,"Error in the list of eigenvectors for %s at pos %d: second index %d is not bigger than %d",listname,pos-startpos,end_number,number);
+                  break;
      }
    ++pos; /* read next character */
    } /*scanner has finished */

diff --git a/src/tools/mk_angndx.c b/src/tools/mk_angndx.c
index d4b3cfda8bfa4c9c07c8c2d4384188b050b7119d..25215fdcefea4656615449f417efc4e145392edd 100644 (file)
--- a/src/tools/mk_angndx.c
+++ b/src/tools/mk_angndx.c
@@ -173,7 +173,7 @@ static int *select_ftype(const char *opt,int *nft,int *mult)
   if (opt[0] == 'a') {
     *mult = 3;
     for(ftype=0; ftype<F_NRE; ftype++) {
-      if (interaction_function[ftype].flags & IF_ATYPE ||
+      if ((interaction_function[ftype].flags & IF_ATYPE) ||
          ftype == F_TABANGLES) {
        (*nft)++;
        srenew(ft,*nft);

diff --git a/src/tools/pp2shift.h b/src/tools/pp2shift.h
index 5736ab85916bf9876bde0656d75bb92f70c1afe0..d61b532eb9f752604cc218be5d96f6ed31aca802 100644 (file)
--- a/src/tools/pp2shift.h
+++ b/src/tools/pp2shift.h
@@ -85,7 +85,7 @@ extern void mk_chi_lookup (int **lookup, int maxchi, real **dih,
 
 extern void get_chi_product_traj (real **dih,int nframes,int nangles, 
                           int nlist,int maxchi, t_dlist dlist[], real time[], 
-                          int **lookup,int *xity,gmx_bool bRb,gmx_bool bNormalize,
+                          int **lookup,int *multiplicity,gmx_bool bRb,gmx_bool bNormalize,
                           real core_frac); 
 
 #endif