Apply re-formatting to C++ in src/ tree.

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_rms.cpp

diff --git a/src/gromacs/gmxana/gmx_rms.cpp b/src/gromacs/gmxana/gmx_rms.cpp
index 43c3419d25c2e3ffa14ec82c3c2fdc63f3f92f8b..52a82a0cf176047a0b07ecb1a5054154c68585a7 100644 (file)
--- a/src/gromacs/gmxana/gmx_rms.cpp
+++ b/src/gromacs/gmxana/gmx_rms.cpp
@@ -241,8 +241,18 @@ int gmx_rms(int argc, char* argv[])
     };
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW, NFILE, fnm,
-                           asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+    if (!parse_common_args(&argc,
+                           argv,
+                           PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
+                           NFILE,
+                           fnm,
+                           asize(pa),
+                           pa,
+                           asize(desc),
+                           desc,
+                           0,
+                           nullptr,
+                           &oenv))
     {
         return 0;
     }
@@ -462,8 +472,7 @@ int gmx_rms(int argc, char* argv[])
     natoms_trx = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
     if (natoms_trx != top.atoms.nr)
     {
-        fprintf(stderr, "\nWARNING: topology has %d atoms, whereas trajectory has %d\n",
-                top.atoms.nr, natoms_trx);
+        fprintf(stderr, "\nWARNING: topology has %d atoms, whereas trajectory has %d\n", top.atoms.nr, natoms_trx);
     }
     natoms = std::min(top.atoms.nr, natoms_trx);
     if (bMat || bBond || bPrev)
@@ -701,7 +710,8 @@ int gmx_rms(int argc, char* argv[])
             gmx_fatal(FARGS,
                       "Second trajectory (%d atoms) does not match the first one"
                       " (%d atoms)",
-                      natoms_trx2, natoms_trx);
+                      natoms_trx2,
+                      natoms_trx);
         }
         frame2 = 0;
         do
@@ -859,8 +869,8 @@ int gmx_rms(int argc, char* argv[])
                 {
                     if (bFile2 || (i < j))
                     {
-                        rmsd_mat[i][j] = calc_similar_ind(ewhat != ewRMSD, irms[0], ind_rms_m,
-                                                          w_rms_m, mat_x[i], mat_x2_j);
+                        rmsd_mat[i][j] = calc_similar_ind(
+                                ewhat != ewRMSD, irms[0], ind_rms_m, w_rms_m, mat_x[i], mat_x2_j);
                         if (rmsd_mat[i][j] > rmsd_max)
                         {
                             rmsd_max = rmsd_mat[i][j];
@@ -972,9 +982,22 @@ int gmx_rms(int argc, char* argv[])
                 fprintf(stderr, "Min and Max value set to resp. %f and %f\n", rmsd_min, rmsd_max);
             }
             sprintf(buf, "%s %s matrix", gn_rms[0], whatname[ewhat]);
-            write_xpm(opt2FILE("-m", NFILE, fnm, "w"), 0, buf, whatlabel[ewhat],
-                      output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat,
-                      tel_mat2, axis, axis2, rmsd_mat, rmsd_min, rmsd_max, rlo, rhi, &nlevels);
+            write_xpm(opt2FILE("-m", NFILE, fnm, "w"),
+                      0,
+                      buf,
+                      whatlabel[ewhat],
+                      output_env_get_time_label(oenv),
+                      output_env_get_time_label(oenv),
+                      tel_mat,
+                      tel_mat2,
+                      axis,
+                      axis2,
+                      rmsd_mat,
+                      rmsd_min,
+                      rmsd_max,
+                      rlo,
+                      rhi,
+                      &nlevels);
             /* Print the distribution of RMSD values */
             if (opt2bSet("-dist", NFILE, fnm))
             {
@@ -1033,9 +1056,22 @@ int gmx_rms(int argc, char* argv[])
                 }
                 sprintf(buf, "%s %s vs. delta t", gn_rms[0], whatname[ewhat]);
                 fp = gmx_ffopen("delta.xpm", "w");
-                write_xpm(fp, 0, buf, "density", output_env_get_time_label(oenv), whatlabel[ewhat],
-                          delta_xsize, del_lev + 1, del_xaxis, del_yaxis, delta, 0.0, delta_max,
-                          rlo, rhi, &nlevels);
+                write_xpm(fp,
+                          0,
+                          buf,
+                          "density",
+                          output_env_get_time_label(oenv),
+                          whatlabel[ewhat],
+                          delta_xsize,
+                          del_lev + 1,
+                          del_xaxis,
+                          del_yaxis,
+                          delta,
+                          0.0,
+                          delta_max,
+                          rlo,
+                          rhi,
+                          &nlevels);
                 gmx_ffclose(fp);
             }
             if (opt2bSet("-bin", NFILE, fnm))
@@ -1068,7 +1104,8 @@ int gmx_rms(int argc, char* argv[])
                 fprintf(stderr,
                         "Bond angle Min and Max set to:\n"
                         "Min. angle: %f, Max. angle: %f\n",
-                        bond_min, bond_max);
+                        bond_min,
+                        bond_max);
             }
             rlo.r = 1;
             rlo.g = 1;
@@ -1077,9 +1114,22 @@ int gmx_rms(int argc, char* argv[])
             rhi.g = 0;
             rhi.b = 0;
             sprintf(buf, "%s av. bond angle deviation", gn_rms[0]);
-            write_xpm(opt2FILE("-bm", NFILE, fnm, "w"), 0, buf, "degrees",
-                      output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat,
-                      tel_mat2, axis, axis2, bond_mat, bond_min, bond_max, rlo, rhi, &nlevels);
+            write_xpm(opt2FILE("-bm", NFILE, fnm, "w"),
+                      0,
+                      buf,
+                      "degrees",
+                      output_env_get_time_label(oenv),
+                      output_env_get_time_label(oenv),
+                      tel_mat,
+                      tel_mat2,
+                      axis,
+                      axis2,
+                      bond_mat,
+                      bond_min,
+                      bond_max,
+                      rlo,
+                      rhi,
+                      &nlevels);
         }
     }
 
@@ -1092,15 +1142,22 @@ int gmx_rms(int argc, char* argv[])
     }
     else
     {
-        sprintf(buf, "%s with frame %g %s ago", whatxvgname[ewhat], time[prev * freq] - time[0],
+        sprintf(buf,
+                "%s with frame %g %s ago",
+                whatxvgname[ewhat],
+                time[prev * freq] - time[0],
                 output_env_get_time_label(oenv).c_str());
     }
-    fp = xvgropen(opt2fn("-o", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
-                  whatxvglabel[ewhat], oenv);
+    fp = xvgropen(opt2fn("-o", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv), whatxvglabel[ewhat], oenv);
     if (output_env_get_print_xvgr_codes(oenv))
     {
-        fprintf(fp, "@ subtitle \"%s%s after %s%s%s\"\n", (nrms == 1) ? "" : "of ", gn_rms[0],
-                fitgraphlabel[efit], bFit ? " to " : "", bFit ? gn_fit : "");
+        fprintf(fp,
+                "@ subtitle \"%s%s after %s%s%s\"\n",
+                (nrms == 1) ? "" : "of ",
+                gn_rms[0],
+                fitgraphlabel[efit],
+                bFit ? " to " : "",
+                bFit ? gn_fit : "");
     }
     if (nrms != 1)
     {
@@ -1135,8 +1192,7 @@ int gmx_rms(int argc, char* argv[])
         {
             if (output_env_get_print_xvgr_codes(oenv))
             {
-                fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n", gn_rms[0],
-                        bFit ? gn_fit : "");
+                fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n", gn_rms[0], bFit ? gn_fit : "");
             }
         }
         else