Fix gmx solvate topology updating

The topology update of gmx solvate was hardcoded to SOL molecules
(and some of the reported quantities also registered HOH and WAT).

Changed to allow updates based on any solvent molecule information.

Also, now allows for updates with multiple solvent molecule types
in the input solvent configuration

Added test case for topology update with multiple solvents

fixes #1929

Change-Id: If506e0f509c8a25cb615fb8d3f15b4dfdb239afa

diff --git a/src/gromacs/gmxpreprocess/solvate.cpp b/src/gromacs/gmxpreprocess/solvate.cpp
index d163e405f3381ab764fe6341f75b4c355af7ec22..e56719cc63bc4bf4f95f5e548ab145edfb435c78 100644 (file)
--- a/src/gromacs/gmxpreprocess/solvate.cpp
+++ b/src/gromacs/gmxpreprocess/solvate.cpp
@@ -729,29 +729,21 @@ static void add_solv(const char *fn, t_topology *top,
     sfree(top_solvt);
 }
 
-static void update_top(t_atoms *atoms, matrix box, int NFILE, t_filenm fnm[],
+static void update_top(t_atoms *atoms, int firstSolventResidueIndex, matrix box, int NFILE, t_filenm fnm[],
                        gmx_atomprop_t aps)
 {
-    FILE       *fpin, *fpout;
-    char        buf[STRLEN], buf2[STRLEN], *temp;
-    const char *topinout;
-    int         line;
-    gmx_bool    bSystem, bMolecules, bSkip;
-    int         i, nsol = 0;
-    double      mtot;
-    real        vol, mm;
-
-    for (i = 0; (i < atoms->nres); i++)
-    {
-        /* calculate number of SOLvent molecules */
-        if ( (strcmp(*atoms->resinfo[i].name, "SOL") == 0) ||
-             (strcmp(*atoms->resinfo[i].name, "WAT") == 0) ||
-             (strcmp(*atoms->resinfo[i].name, "HOH") == 0) )
-        {
-            nsol++;
-        }
-    }
-    mtot = 0;
+    FILE        *fpin, *fpout;
+    char         buf[STRLEN], buf2[STRLEN], *temp;
+    const char  *topinout;
+    int          line;
+    gmx_bool     bSystem;
+    int          i;
+    double       mtot;
+    real         vol, mm;
+
+    int          nsol                     =  atoms->nres - firstSolventResidueIndex;
+
+    mtot                     = 0;
     for (i = 0; (i < atoms->nr); i++)
     {
         gmx_atomprop_query(aps, epropMass,
@@ -765,7 +757,7 @@ static void update_top(t_atoms *atoms, matrix box, int NFILE, t_filenm fnm[],
     fprintf(stderr, "Volume                 :  %10g (nm^3)\n", vol);
     fprintf(stderr, "Density                :  %10g (g/l)\n",
             (mtot*1e24)/(AVOGADRO*vol));
-    fprintf(stderr, "Number of SOL molecules:  %5d   \n\n", nsol);
+    fprintf(stderr, "Number of solvent molecules:  %5d   \n\n", nsol);
 
     /* open topology file and append sol molecules */
     topinout  = ftp2fn(efTOP, NFILE, fnm);
@@ -778,10 +770,9 @@ static void update_top(t_atoms *atoms, matrix box, int NFILE, t_filenm fnm[],
         fpin    = gmx_ffopen(topinout, "r");
         fpout   = gmx_fopen_temporary(temporary_filename);
         line    = 0;
-        bSystem = bMolecules = FALSE;
+        bSystem = FALSE;
         while (fgets(buf, STRLEN, fpin))
         {
-            bSkip = FALSE;
             line++;
             strcpy(buf2, buf);
             if ((temp = strchr(buf2, '\n')) != nullptr)
@@ -803,7 +794,6 @@ static void update_top(t_atoms *atoms, matrix box, int NFILE, t_filenm fnm[],
                     ltrim(buf2);
                     rtrim(buf2);
                     bSystem    = (gmx_strcasecmp(buf2, "system") == 0);
-                    bMolecules = (gmx_strcasecmp(buf2, "molecules") == 0);
                 }
             }
             else if (bSystem && nsol && (buf[0] != ';') )
@@ -816,41 +806,37 @@ static void update_top(t_atoms *atoms, matrix box, int NFILE, t_filenm fnm[],
                     bSystem = FALSE;
                 }
             }
-            else if (bMolecules)
+            fprintf(fpout, "%s", buf);
+        }
+        gmx_ffclose(fpin);
+
+        // Add new solvent molecules to the topology
+        if (nsol > 0)
+        {
+            std::string currRes  = *atoms->resinfo[firstSolventResidueIndex].name;
+            int         resCount = 0;
+
+            // Iterate through solvent molecules and increment a count until new resname found
+            for (int i = firstSolventResidueIndex; i < atoms->nres; i++)
             {
-                /* check if this is a line with solvent molecules */
-                sscanf(buf, "%4095s", buf2);
-                if (strcmp(buf2, "SOL") == 0)
+                if ((currRes.compare(*atoms->resinfo[i].name) == 0))
                 {
-                    sscanf(buf, "%*4095s %20d", &i);
-                    nsol -= i;
-                    if (nsol < 0)
-                    {
-                        bSkip = TRUE;
-                        nsol += i;
-                    }
+                    resCount += 1;
                 }
-            }
-            if (bSkip)
-            {
-                if ((temp = strchr(buf, '\n')) != nullptr)
+                else
                 {
-                    temp[0] = '\0';
+                    // Change topology and restart count
+                    fprintf(stdout, "Adding line for %d solvent molecules with resname (%s) to "
+                            "topology file (%s)\n", resCount, currRes.c_str(), topinout);
+                    fprintf(fpout, "%-15s %5d\n", currRes.c_str(), resCount);
+                    currRes  = *atoms->resinfo[i].name;
+                    resCount = 1;
                 }
-                fprintf(stdout, "Removing line #%d '%s' from topology file (%s)\n",
-                        line, buf, topinout);
-            }
-            else
-            {
-                fprintf(fpout, "%s", buf);
             }
-        }
-        gmx_ffclose(fpin);
-        if (nsol)
-        {
-            fprintf(stdout, "Adding line for %d solvent molecules to "
-                    "topology file (%s)\n", nsol, topinout);
-            fprintf(fpout, "%-15s %5d\n", "SOL", nsol);
+            // One more print needed for last residue type
+            fprintf(stdout, "Adding line for %d solvent molecules with resname (%s) to "
+                    "topology file (%s)\n", resCount, currRes.c_str(), topinout);
+            fprintf(fpout, "%-15s %5d\n", currRes.c_str(), resCount);
         }
         gmx_ffclose(fpout);
         make_backup(topinout);
@@ -935,10 +921,11 @@ int gmx_solvate(int argc, char *argv[])
     };
 #define NFILE asize(fnm)
 
-    real              defaultDistance = 0.105, r_shell = 0, scaleFactor = 0.57;
-    rvec              new_box         = {0.0, 0.0, 0.0};
-    gmx_bool          bReadV          = FALSE;
-    int               max_sol         = 0;
+    real              defaultDistance          = 0.105, r_shell = 0, scaleFactor = 0.57;
+    rvec              new_box                  = {0.0, 0.0, 0.0};
+    gmx_bool          bReadV                   = FALSE;
+    int               max_sol                  = 0;
+    int               firstSolventResidueIndex = 0;
     gmx_output_env_t *oenv;
     t_pargs           pa[]              = {
         { "-box",    FALSE, etRVEC, {new_box},
@@ -992,6 +979,10 @@ int gmx_solvate(int argc, char *argv[])
             fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
             bProt = FALSE;
         }
+        else
+        {
+            firstSolventResidueIndex = top->atoms.nres;
+        }
     }
     if (bBox)
     {
@@ -1020,7 +1011,7 @@ int gmx_solvate(int argc, char *argv[])
     /* print size of generated configuration */
     fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
             top->atoms.nr, top->atoms.nres);
-    update_top(&top->atoms, box, NFILE, fnm, aps);
+    update_top(&top->atoms, firstSolventResidueIndex, box, NFILE, fnm, aps);
 
     gmx_atomprop_destroy(aps);
     done_top(top);

diff --git a/src/gromacs/gmxpreprocess/tests/mixed_solvent.gro b/src/gromacs/gmxpreprocess/tests/mixed_solvent.gro
new file mode 100644 (file)
index 0000000..5c39839
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/mixed_solvent.gro
@@ -0,0 +1,651 @@
+216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
+  648
+    1HOH     OW    1    .230    .628    .113
+    1HOH    HW1    2    .137    .626    .150
+    1HOH    HW2    3    .231    .589    .021
+    2HOH     OW    4    .225    .275   -.866
+    2HOH    HW1    5    .260    .258   -.774
+    2HOH    HW2    6    .137    .230   -.878
+    3HOH     OW    7    .019    .368    .647
+    3HOH    HW1    8   -.063    .411    .686
+    3HOH    HW2    9   -.009    .295    .584
+    4HOH     OW   10    .569   -.587   -.697
+    4HOH    HW1   11    .476   -.594   -.734
+    4HOH    HW2   12    .580   -.498   -.653
+    5HOH     OW   13   -.307   -.351    .703
+    5HOH    HW1   14   -.364   -.367    .784
+    5HOH    HW2   15   -.366   -.341    .623
+    6HOH     OW   16   -.119    .618    .856
+    6HOH    HW1   17   -.086    .712    .856
+    6HOH    HW2   18   -.068    .564    .922
+    7HOH     OW   19   -.727    .703    .717
+    7HOH    HW1   20   -.670    .781    .692
+    7HOH    HW2   21   -.787    .729    .793
+    8HOH     OW   22   -.107    .607    .231
+    8HOH    HW1   23   -.119    .594    .132
+    8HOH    HW2   24   -.137    .526    .280
+    9HOH     OW   25    .768   -.718   -.839
+    9HOH    HW1   26    .690   -.701   -.779
+    9HOH    HW2   27    .802   -.631   -.875
+   10HOH     OW   28    .850    .798   -.039
+   10HOH    HW1   29    .846    .874    .026
+   10HOH    HW2   30    .872    .834   -.130
+   11HOH     OW   31    .685   -.850    .665
+   11HOH    HW1   32    .754   -.866    .735
+   11HOH    HW2   33    .612   -.793    .703
+   12HOH     OW   34    .686   -.701   -.059
+   12HOH    HW1   35    .746   -.622   -.045
+   12HOH    HW2   36    .600   -.670   -.100
+   13HOH     OW   37    .335   -.427   -.801
+   13HOH    HW1   38    .257   -.458   -.854
+   13HOH    HW2   39    .393   -.369   -.858
+   14HOH     OW   40   -.402   -.357   -.523
+   14HOH    HW1   41   -.378   -.263   -.497
+   14HOH    HW2   42   -.418   -.411   -.441
+   15HOH     OW   43    .438    .392   -.363
+   15HOH    HW1   44    .520    .336   -.354
+   15HOH    HW2   45    .357    .334   -.359
+   16HOH     OW   46   -.259    .447    .737
+   16HOH    HW1   47   -.333    .493    .687
+   16HOH    HW2   48   -.208    .515    .790
+   17HOH     OW   49    .231   -.149    .483
+   17HOH    HW1   50    .265   -.072    .537
+   17HOH    HW2   51    .275   -.149    .393
+   18HOH     OW   52   -.735   -.521   -.172
+   18HOH    HW1   53   -.688   -.521   -.084
+   18HOH    HW2   54   -.783   -.608   -.183
+   19HOH     OW   55    .230   -.428    .538
+   19HOH    HW1   56    .204   -.332    .538
+   19HOH    HW2   57    .159   -.482    .583
+   20HOH     OW   58    .240   -.771    .886
+   20HOH    HW1   59    .254   -.855    .938
+   20HOH    HW2   60    .185   -.707    .941
+   21HOH     OW   61    .620   -.076   -.423
+   21HOH    HW1   62    .528   -.093   -.388
+   21HOH    HW2   63    .648    .016   -.397
+   22HOH     OW   64    .606   -.898    .123
+   22HOH    HW1   65    .613   -.814    .069
+   22HOH    HW2   66    .652   -.885    .211
+   23HOH     OW   67   -.268    .114   -.382
+   23HOH    HW1   68   -.286    .181   -.454
+   23HOH    HW2   69   -.271    .160   -.293
+   24HOH     OW   70    .122    .643    .563
+   24HOH    HW1   71    .077    .555    .580
+   24HOH    HW2   72    .121    .697    .647
+   25HOH     OW   73   -.020   -.095    .359
+   25HOH    HW1   74    .034   -.124    .439
+   25HOH    HW2   75    .010   -.005    .330
+   26HOH     OW   76    .027   -.266    .117
+   26HOH    HW1   77    .008   -.362    .138
+   26HOH    HW2   78   -.006   -.208    .192
+   27HOH     OW   79   -.173    .922    .612
+   27HOH    HW1   80   -.078    .893    .620
+   27HOH    HW2   81   -.181    .987    .537
+   28HOH     OW   82   -.221   -.754    .432
+   28HOH    HW1   83   -.135   -.752    .380
+   28HOH    HW2   84   -.207   -.707    .520
+   29HOH     OW   85    .113    .737   -.265
+   29HOH    HW1   86    .201    .724   -.220
+   29HOH    HW2   87    .100    .834   -.287
+   30HOH     OW   88    .613   -.497    .726
+   30HOH    HW1   89    .564   -.584    .735
+   30HOH    HW2   90    .590   -.454    .639
+   31HOH     OW   91   -.569   -.634   -.439
+   31HOH    HW1   92   -.532   -.707   -.497
+   31HOH    HW2   93   -.517   -.629   -.354
+   32HOH     OW   94    .809    .004    .502
+   32HOH    HW1   95    .849    .095    .493
+   32HOH    HW2   96    .709    .012    .508
+   33HOH     OW   97    .197   -.886   -.598
+   33HOH    HW1   98    .286   -.931   -.612
+   33HOH    HW2   99    .124   -.951   -.617
+   34HOH     OW  100   -.337   -.863    .190
+   34HOH    HW1  101   -.400   -.939    .203
+   34HOH    HW2  102   -.289   -.845    .276
+   35HOH     OW  103   -.675   -.070   -.246
+   35HOH    HW1  104   -.651   -.010   -.322
+   35HOH    HW2  105   -.668   -.165   -.276
+   36HOH     OW  106    .317    .251   -.061
+   36HOH    HW1  107    .388    .322   -.055
+   36HOH    HW2  108    .229    .290   -.033
+   37HOH     OW  109   -.396   -.445   -.909
+   37HOH    HW1  110   -.455   -.439   -.829
+   37HOH    HW2  111   -.411   -.533   -.955
+   38HOH     OW  112   -.195   -.148    .572
+   38HOH    HW1  113   -.236   -.171    .484
+   38HOH    HW2  114   -.213   -.222    .637
+   39HOH     OW  115    .598    .729    .270
+   39HOH    HW1  116    .622    .798    .202
+   39HOH    HW2  117    .520    .762    .324
+   40HOH     OW  118   -.581    .345   -.918
+   40HOH    HW1  119   -.667    .295   -.931
+   40HOH    HW2  120   -.519    .291   -.862
+   41HOH     OW  121   -.286   -.200    .307
+   41HOH    HW1  122   -.197   -.154    .310
+   41HOH    HW2  123   -.307   -.224    .212
+   42HOH     OW  124    .807    .605   -.397
+   42HOH    HW1  125    .760    .602   -.308
+   42HOH    HW2  126    .756    .550   -.463
+   43HOH     OW  127   -.468    .469   -.188
+   43HOH    HW1  128   -.488    .512   -.100
+   43HOH    HW2  129   -.390    .407   -.179
+   44HOH     OW  130   -.889    .890   -.290
+   44HOH    HW1  131   -.843    .806   -.319
+   44HOH    HW2  132   -.945    .924   -.365
+   45HOH     OW  133   -.871    .410   -.620
+   45HOH    HW1  134   -.948    .444   -.566
+   45HOH    HW2  135   -.905    .359   -.699
+   46HOH     OW  136   -.821    .701    .429
+   46HOH    HW1  137   -.795    .697    .525
+   46HOH    HW2  138   -.906    .650    .415
+   47HOH     OW  139    .076    .811    .789
+   47HOH    HW1  140    .175    .799    .798
+   47HOH    HW2  141    .052    .906    .810
+   48HOH     OW  142    .130   -.041   -.291
+   48HOH    HW1  143    .120   -.056   -.192
+   48HOH    HW2  144    .044   -.005   -.327
+   49HOH     OW  145    .865    .348    .195
+   49HOH    HW1  146    .924    .411    .146
+   49HOH    HW2  147    .884    .254    .166
+   50HOH     OW  148   -.143    .585   -.031
+   50HOH    HW1  149   -.169    .674   -.067
+   50HOH    HW2  150   -.145    .517   -.104
+   51HOH     OW  151   -.500   -.718    .545
+   51HOH    HW1  152   -.417   -.747    .497
+   51HOH    HW2  153   -.549   -.651    .489
+   52HOH     OW  154    .550    .196    .885
+   52HOH    HW1  155    .545    .191    .985
+   52HOH    HW2  156    .552    .292    .856
+   53HOH     OW  157   -.854   -.406    .477
+   53HOH    HW1  158   -.900   -.334    .425
+   53HOH    HW2  159   -.858   -.386    .575
+   54HOH     OW  160    .351   -.061    .853
+   54HOH    HW1  161    .401   -.147    .859
+   54HOH    HW2  162    .416    .016    .850
+   55HOH     OW  163   -.067   -.796    .873
+   55HOH    HW1  164   -.129   -.811    .797
+   55HOH    HW2  165   -.119   -.785    .958
+   56HOH     OW  166   -.635   -.312   -.356
+   56HOH    HW1  167   -.629   -.389   -.292
+   56HOH    HW2  168   -.687   -.338   -.436
+   57HOH     OW  169    .321   -.919    .242
+   57HOH    HW1  170    .403   -.880    .200
+   57HOH    HW2  171    .294  -1.001    .193
+   58HOH     OW  172   -.404    .735    .728
+   58HOH    HW1  173   -.409    .670    .803
+   58HOH    HW2  174   -.324    .794    .741
+   59HOH     OW  175    .461   -.596   -.135
+   59HOH    HW1  176    .411   -.595   -.221
+   59HOH    HW2  177    .398   -.614   -.059
+   60HOH     OW  178   -.751   -.086    .237
+   60HOH    HW1  179   -.811   -.148    .287
+   60HOH    HW2  180   -.720   -.130    .152
+   61HOH     OW  181    .202    .285   -.364
+   61HOH    HW1  182    .122    .345   -.377
+   61HOH    HW2  183    .192    .236   -.278
+   62HOH     OW  184   -.230   -.485    .081
+   62HOH    HW1  185   -.262   -.391    .071
+   62HOH    HW2  186   -.306   -.548    .069
+   63HOH     OW  187    .464   -.119    .323
+   63HOH    HW1  188    .497   -.080    .409
+   63HOH    HW2  189    .540   -.126    .258
+   64HOH     OW  190   -.462    .107    .426
+   64HOH    HW1  191   -.486    .070    .336
+   64HOH    HW2  192   -.363    .123    .430
+   65HOH     OW  193    .249   -.077   -.621
+   65HOH    HW1  194    .306   -.142   -.571
+   65HOH    HW2  195    .233   -.110   -.714
+   66HOH     OW  196   -.922   -.164    .904
+   66HOH    HW1  197   -.842   -.221    .925
+   66HOH    HW2  198   -.971   -.204    .827
+   67HOH     OW  199    .382    .700    .480
+   67HOH    HW1  200    .427    .610    .477
+   67HOH    HW2  201    .288    .689    .513
+   68HOH     OW  202   -.315    .222   -.133
+   68HOH    HW1  203   -.320    .259   -.041
+   68HOH    HW2  204   -.387    .153   -.145
+   69HOH     OW  205    .614    .122    .117
+   69HOH    HW1  206    .712    .100    .124
+   69HOH    HW2  207    .583    .105    .024
+   70HOH     OW  208    .781    .264   -.113
+   70HOH    HW1  209    .848    .203   -.070
+   70HOH    HW2  210    .708    .283   -.048
+   71HOH     OW  211    .888   -.348   -.667
+   71HOH    HW1  212    .865   -.373   -.761
+   71HOH    HW2  213    .949   -.417   -.628
+   72HOH     OW  214   -.511    .590   -.429
+   72HOH    HW1  215   -.483    .547   -.344
+   72HOH    HW2  216   -.486    .686   -.428
+   73HOH     OW  217    .803   -.460    .924
+   73HOH    HW1  218    .893   -.446    .882
+   73HOH    HW2  219    .732   -.458    .853
+   74HOH     OW  220    .922    .503    .899
+   74HOH    HW1  221    .897    .494    .803
+   74HOH    HW2  222    .970    .421    .930
+   75HOH     OW  223    .539    .064    .512
+   75HOH    HW1  224    .458    .065    .570
+   75HOH    HW2  225    .542    .147    .457
+   76HOH     OW  226   -.428   -.674    .041
+   76HOH    HW1  227   -.396   -.750    .098
+   76HOH    HW2  228   -.520   -.647    .071
+   77HOH     OW  229    .297    .035    .171
+   77HOH    HW1  230    .346    .119    .150
+   77HOH    HW2  231    .359   -.030    .216
+   78HOH     OW  232   -.927    .236    .480
+   78HOH    HW1  233   -.975    .277    .402
+   78HOH    HW2  234   -.828    .234    .461
+   79HOH     OW  235   -.786    .683   -.398
+   79HOH    HW1  236   -.866    .622   -.395
+   79HOH    HW2  237   -.705    .630   -.422
+   80HOH     OW  238   -.635   -.292    .793
+   80HOH    HW1  239   -.614   -.218    .728
+   80HOH    HW2  240   -.567   -.292    .866
+   81HOH     OW  241    .459   -.710    .741
+   81HOH    HW1  242    .388   -.737    .806
+   81HOH    HW2  243    .433   -.738    .648
+   82HOH     OW  244   -.591   -.065    .591
+   82HOH    HW1  245   -.547   -.001    .527
+   82HOH    HW2  246   -.641   -.013    .661
+   83HOH     OW  247   -.830    .549    .016
+   83HOH    HW1  248   -.871    .631   -.023
+   83HOH    HW2  249   -.766    .575    .089
+   84HOH     OW  250    .078    .556   -.476
+   84HOH    HW1  251    .170    .555   -.517
+   84HOH    HW2  252    .072    .630   -.409
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diff --git a/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_update_Topology_Works.xml b/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_update_Topology_Works.xml
new file mode 100644 (file)
index 0000000..257368b
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_update_Topology_Works.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-o">
+      <GroFile Name="Header">
+        <String Name="Title">Test system for solvate</String>
+        <Int Name="Number of atoms">12141</Int>
+      </GroFile>
+    </File>
+    <File Name="-p">
+      <String Name="Contents"><![CDATA[
+[ system ]
+; Name
+simple system in water
+
+[ molecules ]
+; Compound  #mols
+A         1
+B         1
+HOH              1876
+SOL              2169
+]]></String>
+    </File>
+  </OutputFiles>
+</ReferenceData>
\ No newline at end of file

diff --git a/src/gromacs/gmxpreprocess/tests/simple.gro b/src/gromacs/gmxpreprocess/tests/simple.gro
new file mode 100644 (file)
index 0000000..c178a75
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/simple.gro
@@ -0,0 +1,9 @@
+Test system for solvate
+ 6
+    1A      A1    1   1.000   1.000   0.000
+    1A      A2    2   1.000   2.000   0.000
+    1A      A3    3   1.000   3.000   0.000
+    2B      B1    4   1.000   4.000   1.000
+    2B      B2    5   2.000   1.000   2.000
+    2B      B3    6   2.000   2.000   3.000
+  5.00000   5.00000   5.00000

diff --git a/src/gromacs/gmxpreprocess/tests/simple.top b/src/gromacs/gmxpreprocess/tests/simple.top
new file mode 100644 (file)
index 0000000..03ce9c3
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/simple.top
@@ -0,0 +1,8 @@
+[ system ]
+; Name
+simple system
+
+[ molecules ]
+; Compound  #mols
+A         1
+B         1

diff --git a/src/gromacs/gmxpreprocess/tests/solvate.cpp b/src/gromacs/gmxpreprocess/tests/solvate.cpp
index f1858fc9b538b1b2f596c46eafcb03f1f8da0746..cbcc89385d52a40669547b95598840c3dca6d964 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/solvate.cpp
+++ b/src/gromacs/gmxpreprocess/tests/solvate.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -58,6 +58,7 @@ namespace
 
 using gmx::test::CommandLine;
 using gmx::test::ConfMatch;
+using gmx::test::ExactTextMatch;
 
 class SolvateTest : public gmx::test::CommandLineTestBase
 {
@@ -125,4 +126,24 @@ TEST_F(SolvateTest, shell_Works)
     runTest(CommandLine(cmdline));
 }
 
+TEST_F(SolvateTest, update_Topology_Works)
+{
+    // use solvent box with 2 solvents, check that topology has been updated
+    const char *const cmdline[] = {
+        "solvate"
+    };
+    setInputFile("-cs", "mixed_solvent.gro");
+    setInputFile("-cp", "simple.gro");
+
+    // TODO: Consider adding a convenience method for this.
+    // Copies topology file to where it would be found as an output file, so the copied
+    // .top file is used as both input and output
+    std::string topFileName           = fileManager().getInputFilePath("simple.top");
+    std::string modifiableTopFileName = fileManager().getTemporaryFilePath("simple.top");
+    gmx_file_copy(topFileName.c_str(), modifiableTopFileName.c_str(), true);
+    setOutputFile("-p", "simple.top", ExactTextMatch());
+
+    runTest(CommandLine(cmdline));
+}
+
 } // namespace