Merge "v-rescale works with tau-t >= 0" into release-4-6

diff --git a/include/mdrun.h b/include/mdrun.h
index 1373bfd55eaa0d0bcfb88aba99e2eb16587e8b76..a11fa78ac34145c2bdf2f912be8dc3e1e9e941e7 100644 (file)
--- a/include/mdrun.h
+++ b/include/mdrun.h
@@ -215,7 +215,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
              real rdd, real rconstr, const char *dddlb_opt, real dlb_scale,
              const char *ddcsx, const char *ddcsy, const char *ddcsz,
              const char *nbpu_opt,
-             int nsteps_cmdline, int nstepout, int resetstep,
+             gmx_large_int_t nsteps_cmdline, int nstepout, int resetstep,
              int nmultisim, int repl_ex_nst, int repl_ex_nex,
              int repl_ex_seed, real pforce, real cpt_period, real max_hours,
              const char *deviceOptions, unsigned long Flags);

diff --git a/src/gmxlib/selection/compiler.c b/src/gmxlib/selection/compiler.c
index 0ccb548d3e2a7902c927c06433b8747680fda2b7..326635cdd0d866d1e463d5b5d70bdeb1706de4f9 100644 (file)
--- a/src/gmxlib/selection/compiler.c
+++ b/src/gmxlib/selection/compiler.c
@@ -314,8 +314,15 @@ enum
     SEL_CDATA_MINMAXALLOC = 16,
     /** Whether subexpressions use simple pass evaluation functions. */
     SEL_CDATA_SIMPLESUBEXPR = 32,
-    /** Whether this expressions is a part of a common subexpression. */
-    SEL_CDATA_COMMONSUBEXPR = 64
+    /*! \brief
+     * Whether a static subexpression needs to support multiple evaluations.
+     *
+     * This flag may only be set on \ref SEL_SUBEXPR elements that also have
+     * SEL_CDATA_SIMPLESUBEXPR.
+     */
+    SEL_CDATA_STATICMULTIEVALSUBEXPR = 64,
+    /** Whether this expression is a part of a common subexpression. */
+    SEL_CDATA_COMMONSUBEXPR = 128
 };
 
 /*! \internal \brief
@@ -397,6 +404,10 @@ _gmx_selelem_print_compiler_info(FILE *fp, t_selelem *sel, int level)
     {
         fprintf(fp, "Ss");
     }
+    if (sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR)
+    {
+        fprintf(fp, "Sm");
+    }
     if (sel->cdata->flags & SEL_CDATA_COMMONSUBEXPR)
     {
         fprintf(fp, "Sc");
@@ -1102,19 +1113,25 @@ init_item_evalfunc(t_selelem *sel)
             break;
 
         case SEL_SUBEXPR:
-            sel->evaluate = (sel->refcount == 2
-                             ? &_gmx_sel_evaluate_subexpr_simple
-                             : &_gmx_sel_evaluate_subexpr);
+            if (sel->refcount == 2
+                && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
+            {
+                sel->evaluate = &_gmx_sel_evaluate_subexpr_simple;
+            }
+            else
+            {
+                sel->evaluate = &_gmx_sel_evaluate_subexpr;
+            }
             break;
 
         case SEL_SUBEXPRREF:
             sel->name     = sel->child->name;
-            sel->evaluate = (sel->child->refcount == 2
+            sel->evaluate = ((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
                              ? &_gmx_sel_evaluate_subexprref_simple
                              : &_gmx_sel_evaluate_subexprref);
             break;
     }
-
+    sel->cdata->evaluate = sel->evaluate;
     return TRUE;
 }
 
@@ -1179,7 +1196,8 @@ init_item_evaloutput(t_selelem *sel)
         }
     }
 
-    if (sel->type == SEL_SUBEXPR && sel->refcount == 2)
+    if (sel->type == SEL_SUBEXPR && sel->refcount == 2
+        && !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
     {
         sel->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
         if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
@@ -1199,7 +1217,8 @@ init_item_evaloutput(t_selelem *sel)
             _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
         }
     }
-    else if (sel->type == SEL_SUBEXPRREF && sel->child->refcount == 2)
+    else if (sel->type == SEL_SUBEXPRREF
+             && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR))
     {
         if (sel->v.u.ptr)
         {
@@ -1361,6 +1380,15 @@ init_item_staticeval(t_selelem *sel)
                     init_item_staticeval(child);
                 }
             }
+            /* If an expression is evaluated for a dynamic group, then also
+             * atom-valued parameters need to be evaluated every time. */
+            if ((sel->flags & SEL_DYNAMIC)
+                && (sel->type == SEL_EXPRESSION || sel->type == SEL_MODIFIER)
+                && (child->flags & SEL_ATOMVAL))
+            {
+                child->flags        |= SEL_DYNAMIC;
+                child->cdata->flags &= ~SEL_CDATA_STATIC;
+            }
             child = child->next;
         }
     }
@@ -1417,7 +1445,17 @@ init_item_subexpr_flags(t_selelem *sel)
     }
     else if (sel->type == SEL_SUBEXPRREF && sel->child->refcount == 2)
     {
-        sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
+        /* See similar condition in init_item_staticeval(). */
+        if ((sel->flags & SEL_ATOMVAL)
+            && (sel->flags & SEL_DYNAMIC)
+            && !(sel->child->flags & SEL_DYNAMIC))
+        {
+            sel->child->cdata->flags |= SEL_CDATA_STATICMULTIEVALSUBEXPR;
+        }
+        else
+        {
+            sel->cdata->flags |= SEL_CDATA_SIMPLESUBEXPR;
+        }
     }
 
     /* Process children, but only follow subexpression references if the
@@ -2180,7 +2218,9 @@ analyze_static(gmx_sel_evaluate_t *data, t_selelem *sel, gmx_ana_index_t *g)
             break;
 
         case SEL_SUBEXPR:
-            if (sel->cdata->flags & (SEL_CDATA_SIMPLESUBEXPR | SEL_CDATA_FULLEVAL))
+            if (((sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR) &&
+                 !(sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
+                || (sel->cdata->flags & SEL_CDATA_FULLEVAL))
             {
                 rc = sel->cdata->evaluate(data, sel, g);
                 _gmx_selvalue_setstore(&sel->v, sel->child->v.u.ptr);
@@ -2491,6 +2531,17 @@ postprocess_item_subexpressions(t_selelem *sel)
         sel->child->flags   &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
         sel->child->v.nalloc = -1;
     }
+
+    /* For static subexpressions with a dynamic evaluation group, there is
+     * no need to evaluate them again, as the SEL_SUBEXPRREF takes care of
+     * everything during evaluation. */
+    if (sel->type == SEL_SUBEXPR
+        && (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
+        && (sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
+    {
+        sel->evaluate        = NULL;
+        sel->cdata->evaluate = NULL;
+    }
 }
 
 
@@ -2735,24 +2786,37 @@ gmx_ana_selcollection_compile(gmx_ana_selcollection_t *sc)
             /* FIXME: Clean up the collection */
             return -1;
         }
-        /* Initialize evaluation function. */
-        if (!init_item_evalfunc(item))
-        {
-            /* FIXME: Clean up the collection */
-            return -1;
-        }
-        setup_memory_pooling(item, sc->mempool);
         /* Initialize the compiler data */
         init_item_compilerdata(item);
+        item = item->next;
+    }
+    /* Initialize the static evaluation compiler flags.
+     * Requires the FULLEVAL compiler flag for the whole tree. */
+    item = sc->root;
+    while (item)
+    {
         init_item_staticeval(item);
         item = item->next;
     }
-    /* Initialize subexpression flags and evaluation output.
+    /* Initialize subexpression flags.
      * Requires compiler flags for the full tree. */
     item = sc->root;
     while (item)
     {
         init_item_subexpr_flags(item);
+        item = item->next;
+    }
+    /* Initialize evaluation.
+     * Requires subexpression flags. */
+    item = sc->root;
+    while (item)
+    {
+        if (!init_item_evalfunc(item))
+        {
+            /* FIXME: Clean up the collection */
+            return -1;
+        }
+        setup_memory_pooling(item, sc->mempool);
         init_item_evaloutput(item);
         item = item->next;
     }

diff --git a/src/gmxlib/selection/evaluate.c b/src/gmxlib/selection/evaluate.c
index b77a93eff301999a6eb7d20ab5b2af6d9fe43495..bd09533686c037012d9f1858862fac8d007b19af 100644 (file)
--- a/src/gmxlib/selection/evaluate.c
+++ b/src/gmxlib/selection/evaluate.c
@@ -220,7 +220,8 @@ gmx_ana_selcollection_evaluate(gmx_ana_selcollection_t *sc,
     while (sel)
     {
         /* Clear the evaluation group of subexpressions */
-        if (sel->child && sel->child->type == SEL_SUBEXPR)
+        if (sel->child && sel->child->type == SEL_SUBEXPR
+            && sel->child->evaluate != NULL)
         {
             sel->child->u.cgrp.isize = 0;
             /* Not strictly necessary, because the value will be overwritten
@@ -664,7 +665,7 @@ _gmx_sel_evaluate_subexprref(gmx_sel_evaluate_t *data, t_selelem *sel, gmx_ana_i
     t_selelem *expr;
     int        i, j;
 
-    if (g)
+    if (g != NULL && sel->child->evaluate != NULL)
     {
         int rc;
 

diff --git a/src/kernel/mdrun.c b/src/kernel/mdrun.c
index 8640ee3e016e9db15d8f19f9928f13708839e974..a5c0e6a6256def6a24b6b0bb702c5eef114b58c5 100644 (file)
--- a/src/kernel/mdrun.c
+++ b/src/kernel/mdrun.c
@@ -431,7 +431,7 @@ int cmain(int argc, char *argv[])
     int           repl_ex_nex   = 0;
     int           nstepout      = 100;
     int           resetstep     = -1;
-    int           nsteps        = -2; /* the value -2 means that the mdp option will be used */
+    gmx_large_int_t nsteps      = -2; /* the value -2 means that the mdp option will be used */
 
     rvec          realddxyz          = {0, 0, 0};
     const char   *ddno_opt[ddnoNR+1] =
@@ -521,7 +521,7 @@ int cmain(int argc, char *argv[])
           "Keep and number checkpoint files" },
         { "-append",  FALSE, etBOOL, {&bAppendFiles},
           "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
-        { "-nsteps",  FALSE, etINT, {&nsteps},
+        { "-nsteps",  FALSE, etGMX_LARGE_INT, {&nsteps},
           "Run this number of steps, overrides .mdp file option" },
         { "-maxh",   FALSE, etREAL, {&max_hours},
           "Terminate after 0.99 times this time (hours)" },

diff --git a/src/kernel/runner.c b/src/kernel/runner.c
index 9c0cae32346428955193f00ea9009067094cf727..765be55653ee82ab5793a832b38605b15d323025 100644 (file)
--- a/src/kernel/runner.c
+++ b/src/kernel/runner.c
@@ -131,7 +131,7 @@ struct mdrunner_arglist
     const char     *ddcsy;
     const char     *ddcsz;
     const char     *nbpu_opt;
-    int             nsteps_cmdline;
+    gmx_large_int_t nsteps_cmdline;
     int             nstepout;
     int             resetstep;
     int             nmultisim;
@@ -193,7 +193,8 @@ static t_commrec *mdrunner_start_threads(gmx_hw_opt_t *hw_opt,
                                          const char *dddlb_opt, real dlb_scale,
                                          const char *ddcsx, const char *ddcsy, const char *ddcsz,
                                          const char *nbpu_opt,
-                                         int nsteps_cmdline, int nstepout, int resetstep,
+                                         gmx_large_int_t nsteps_cmdline,
+                                         int nstepout, int resetstep,
                                          int nmultisim, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
                                          real pforce, real cpt_period, real max_hours,
                                          const char *deviceOptions, unsigned long Flags)
@@ -865,10 +866,12 @@ static void check_and_update_hw_opt(gmx_hw_opt_t *hw_opt,
 
 /* Override the value in inputrec with value passed on the command line (if any) */
 static void override_nsteps_cmdline(FILE            *fplog,
-                                    int              nsteps_cmdline,
+                                    gmx_large_int_t  nsteps_cmdline,
                                     t_inputrec      *ir,
                                     const t_commrec *cr)
 {
+    char sbuf[STEPSTRSIZE];
+
     assert(ir);
     assert(cr);
 
@@ -880,13 +883,14 @@ static void override_nsteps_cmdline(FILE            *fplog,
         ir->nsteps = nsteps_cmdline;
         if (EI_DYNAMICS(ir->eI))
         {
-            sprintf(stmp, "Overriding nsteps with value passed on the command line: %d steps, %.3f ps",
-                    nsteps_cmdline, nsteps_cmdline*ir->delta_t);
+            sprintf(stmp, "Overriding nsteps with value passed on the command line: %s steps, %.3f ps",
+                    gmx_step_str(nsteps_cmdline, sbuf),
+                    nsteps_cmdline*ir->delta_t);
         }
         else
         {
-            sprintf(stmp, "Overriding nsteps with value passed on the command line: %d steps",
-                    nsteps_cmdline);
+            sprintf(stmp, "Overriding nsteps with value passed on the command line: %s steps",
+                    gmx_step_str(nsteps_cmdline, sbuf));
         }
 
         md_print_warn(cr, fplog, "%s\n", stmp);
@@ -909,7 +913,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
              const char *dddlb_opt, real dlb_scale,
              const char *ddcsx, const char *ddcsy, const char *ddcsz,
              const char *nbpu_opt,
-             int nsteps_cmdline, int nstepout, int resetstep,
+             gmx_large_int_t nsteps_cmdline, int nstepout, int resetstep,
              int nmultisim, int repl_ex_nst, int repl_ex_nex,
              int repl_ex_seed, real pforce, real cpt_period, real max_hours,
              const char *deviceOptions, unsigned long Flags)

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index b2ff2035a63b816d637815499013a6819c8d2076..bfff897320c17834d86130455197d17f1f21f5f2 100644 (file)
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -42,17 +42,29 @@ if(REGRESSIONTEST_DOWNLOAD AND CMAKE_VERSION VERSION_LESS "2.8.2")
         "REGRESSIONTEST_DOWNLOAD not supported with cmake ${CMAKE_VERSION}" FORCE)
 endif()
 if(REGRESSIONTEST_DOWNLOAD)
-    if(NOT REGRESSIONTEST_VERSION)
-        message(FATAL_ERROR "The configuration files do not specify what regressiontests tarball is suitable for automated download and testing. Please obtain and use a suitable set of tests yourself.")
+    if("${PROJECT_VERSION}" MATCHES "-dev")
+       if("${PROJECT_VERSION}" MATCHES "^5[.]")
+          set(REGRESSIONTEST_URL http://gerrit.gromacs.org/snapshot/refs/heads/master)
+       else()
+          set(REGRESSIONTEST_URL http://gerrit.gromacs.org/snapshot/refs/heads/release-4-6)
+      endif()
+      set(REGRESSIONTEST_PATH "${CMAKE_CURRENT_BINARY_DIR}/regressiontests"
+           CACHE PATH "Path to auto-downloaded regressiontests" FORCE)
+    else()
+        if(NOT REGRESSIONTEST_VERSION)
+          message(FATAL_ERROR "The configuration files do not specify what regressiontests tarball is suitable for automated download and testing. Please obtain and use a suitable set of tests yourself.")
+        endif()
+        set(REGRESSIONTEST_URL http://gerrit.gromacs.org/download/regressiontests-${REGRESSIONTEST_VERSION}.tar.gz)
+        set(REGRESSIONTEST_PATH
+           "${CMAKE_CURRENT_BINARY_DIR}/regressiontests-${REGRESSIONTEST_VERSION}"
+           CACHE PATH "Path to auto-downloaded regressiontests" FORCE)
     endif()
-    set(REGRESSIONTEST_URL
-        http://gerrit.gromacs.org/download/regressiontests-${REGRESSIONTEST_VERSION}.tar.gz)
     set(REGRESSIONTEST_FILE "${CMAKE_CURRENT_BINARY_DIR}/regressiontests.tgz")
     message("Downloading: ${REGRESSIONTEST_URL}")
     file(DOWNLOAD ${REGRESSIONTEST_URL} "${REGRESSIONTEST_FILE}" SHOW_PROGRESS STATUS status LOG log)
     list(GET status 0 status_code)
     list(GET status 1 status_string)
-    
+
     if(NOT status_code EQUAL 0)
         message(FATAL_ERROR "error: downloading '${REGRESSIONTEST_URL}' failed
 status_code: ${status_code}
@@ -60,9 +72,6 @@ status_string: ${status_string}
 log: ${log}")
     endif()
 
-    set(REGRESSIONTEST_PATH
-        "${CMAKE_CURRENT_BINARY_DIR}/regressiontests-${REGRESSIONTEST_VERSION}"
-        CACHE PATH "Path to auto-downloaded regressiontests" FORCE)
     file(REMOVE_RECURSE "${REGRESSIONTEST_PATH}") #delete potential prior folder
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xf "${REGRESSIONTEST_FILE}"
         WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")