Changeset 0fc0b5 for molecuilder/src/builder.cpp

Timestamp:

Aug 7, 2009, 9:13:21 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

ef5521

Parents:

8f9a8e

Message:

Test case of filling a simulation domain with water included.

File:

• molecuilder/src/builder.cpp (modified) (4 diffs)

molecuilder/src/builder.cpp

@@ -1348 +1348 @@
             cout << "\t-A <source>\tCreate adjacency list from bonds parsed from 'dbond'-style file." <<endl;
             cout << "\t-b xx xy xz yy yz zz\tCenter atoms in domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl;
-            cout << "\t-B <basis>\tSetting basis to store to MPQC config files." << endl;
+            cout << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl;
             cout << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
             cout << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl;
@@ -1358 +1358 @@
             cout << "\t-h/-H/-?\tGive this help screen." << endl;
             cout << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
+            cout << "\t-M <basis>\tSetting basis to store to MPQC config files." << endl;
             cout << "\t-n\tFast parsing (i.e. no trajectories are looked for)." << endl;
             cout << "\t-N <radius> <file>\tGet non-convex-envelope." << endl;
@@ -1506 +1507 @@
         if (config_present == present) {
           switch(argv[argptr-1][1]) {
-            case 'B':
+            case 'M':
               if ((argptr >= argc) || (argv[argptr][0] == '-')) {
                 ExitFlag = 255;
@@ -1767 +1768 @@
                 // center
                 mol->CenterInBox((ofstream *)&cout);
+                argptr+=6;
+              }
+              break;
+            case 'B':
+              ExitFlag = 1;
+              if ((argptr+5 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])) || (!IsValidNumber(argv[argptr+2])) || (!IsValidNumber(argv[argptr+3])) || (!IsValidNumber(argv[argptr+4])) || (!IsValidNumber(argv[argptr+5])) ) {
+                ExitFlag = 255;
+                cerr << "Not enough or invalid arguments given for bounding in box: -B <xx> <xy> <xz> <yy> <yz> <zz>" << endl;
+              } else {
+                SaveFlag = true;
+                j = -1;
+                cout << Verbose(1) << "Centering atoms in config file within given simulation box." << endl;
+                for (int i=0;i<6;i++) {
+                  mol->cell_size[i] = atof(argv[argptr+i]);
+                }
+                // center
+                mol->BoundInBox((ofstream *)&cout);
                 argptr+=6;
               }