Support load/save of NBO info

diff --git a/MolLib/Molecule.c b/MolLib/Molecule.c
index 5b80f62..0ff5985 100755 (executable)
--- a/MolLib/Molecule.c
+++ b/MolLib/Molecule.c
@@ -859,11 +859,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* idx symop symbase */
                                if (sscanf(buf, "%d %d %d", &ibuf[0], &ibuf[1], &ibuf[2]) < 3) {
                                        s_append_asprintf(errbuf, "line %d: symmetry operations cannot be read for atom %d", lineNumber, i + 1);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: too many atomic symmetry info\n", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                ap = ATOM_AT_INDEX(mp->atoms, i);
                                ap->symop.sym = ibuf[1] / 1000000;
@@ -884,11 +884,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* idx fix_force fix_pos */
                                if (sscanf(buf, "%d %lf %lf %lf %lf", &ibuf[0], &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3]) < 5) {
                                        s_append_asprintf(errbuf, "line %d: fix atom info cannot be read for atom %d", lineNumber, i + 1);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: too many fix atom info\n", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                ap = ATOM_AT_INDEX(mp->atoms, i);
                                ap->fix_force = dbuf[0];
@@ -908,11 +908,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* idx uff_type */
                                if (sscanf(buf, "%d %6s", &ibuf[0], cbuf[0]) < 2) {
                                        s_append_asprintf(errbuf, "line %d: uff type info cannot be read for atom %d", lineNumber, i + 1);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: too many uff type info\n", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                ap = ATOM_AT_INDEX(mp->atoms, i);
                                strncpy(ap->uff_type, cbuf[0], 5);
@@ -929,11 +929,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* idx mm_exclude periodic_exclude */
                                if (sscanf(buf, "%d %d %d", &ibuf[0], &ibuf[1], &ibuf[2]) < 3) {
                                        s_append_asprintf(errbuf, "line %d: mm_exclude flags cannot be read for atom %d", lineNumber, i + 1);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: too many mm_exclude flags\n", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                ap = ATOM_AT_INDEX(mp->atoms, i);
                                ap->mm_exclude = (ibuf[1] != 0);
@@ -950,7 +950,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* idx count */
                                if ((j = sscanf(buf, "%d %d", &ibuf[0], &ibuf[1])) < 2) {
                                        s_append_asprintf(errbuf, "line %d: bad format for pi_anchor", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                i = ibuf[0];
                                ap = ATOM_AT_INDEX(mp->atoms, i);
@@ -963,7 +963,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                ap->anchor = (PiAnchor *)calloc(sizeof(PiAnchor), 1);
                                if (ibuf[1] < 2 || ibuf[1] >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: bad number of components for pi_anchor", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                AtomConnectResize(&ap->anchor->connect, ibuf[1]);
                                ip = AtomConnectData(&ap->anchor->connect);
@@ -976,15 +976,15 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        }
                                        if (sscanf(buf, "%d %lf", &ibuf[0], &dbuf[0]) < 2) {
                                                s_append_asprintf(errbuf, "line %d: bad format for pi_anchor", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        if (ibuf[0] < 0 || ibuf[0] >= mp->natoms) {
                                                s_append_asprintf(errbuf, "line %d: atom index out of range", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        if (dbuf[0] <= 0.0) {
                                                s_append_asprintf(errbuf, "line %d: the pi anchor weights should be positive", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        ip[i] = ibuf[0];
                                        ap->anchor->coeffs[i] = dbuf[0];
@@ -1005,11 +1005,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                }
                                if (j > 4 && nframes != 0) {
                                        s_append_asprintf(errbuf, "line %d: atom position sigma can only be given for frame 0", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (j > 4 && j != 7) {
                                        s_append_asprintf(errbuf, "line %d: atom position sigma cannot be read for atom %d frame %d", lineNumber, i + 1, nframes);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: too many atom position records\n", lineNumber);
@@ -1050,7 +1050,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                i = sscanf(buf, "%d %d %d %d %d %d %d %d", &ibuf[0], &ibuf[1], &ibuf[2], &ibuf[3], &ibuf[4], &ibuf[5], &ibuf[6], &ibuf[7]);
                                if (i < 2 || i % 2 != 0) {
                                        s_append_asprintf(errbuf, "line %d: bad bond format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                for (j = 0; j < i; j += 2) {
                                        iibuf[0] = ibuf[j];
@@ -1079,7 +1079,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                i = sscanf(buf, "%lf %lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3]);
                                if (i == 0) {
                                        s_append_asprintf(errbuf, "line %d: bad bond order format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                for (j = 0; j < i; j++) {
                                        AssignArray(&mp->bondOrders, &mp->nbondOrders, sizeof(Double), mp->nbondOrders, &dbuf[j]);
@@ -1109,7 +1109,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                i = sscanf(buf, "%d %d %d %d %d %d %d %d %d", &ibuf[0], &ibuf[1], &ibuf[2], &ibuf[3], &ibuf[4], &ibuf[5], &ibuf[6], &ibuf[7], &ibuf[8]);
                                if (i == 0 || i % 3 != 0) {
                                        s_append_asprintf(errbuf, "line %d: bad angle format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                for (j = 0; j < i; j += 3) {
                                        iibuf[0] = ibuf[j];
@@ -1140,7 +1140,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                i = sscanf(buf, "%d %d %d %d %d %d %d %d", &ibuf[0], &ibuf[1], &ibuf[2], &ibuf[3], &ibuf[4], &ibuf[5], &ibuf[6], &ibuf[7]);
                                if (i == 0 || i % 4 != 0) {
                                        s_append_asprintf(errbuf, "line %d: bad dihedral format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                for (j = 0; j < i; j += 4) {
                                        iibuf[0] = ibuf[j];
@@ -1172,7 +1172,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                i = sscanf(buf, "%d %d %d %d %d %d %d %d", &ibuf[0], &ibuf[1], &ibuf[2], &ibuf[3], &ibuf[4], &ibuf[5], &ibuf[6], &ibuf[7]);
                                if (i == 0 || i % 4 != 0) {
                                        s_append_asprintf(errbuf, "line %d: bad improper format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                for (j = 0; j < i; j += 4) {
                                        iibuf[0] = ibuf[j];
@@ -1203,17 +1203,17 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* a b c alpha beta gamma [sigmaflag] */ 
                                if ((j = sscanf(buf, "%lf %lf %lf %lf %lf %lf %d", &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3], &dbuf[4], &dbuf[5], &ibuf[0])) < 6) {
                                        s_append_asprintf(errbuf, "line %d: bad xtalcell format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                MoleculeSetCell(mp, dbuf[0], dbuf[1], dbuf[2], dbuf[3], dbuf[4], dbuf[5], 0);
                                if (j == 7 && ibuf[0] != 0) {
                                        if (ReadLine(buf, sizeof buf, fp, &lineNumber) <= 0) {
                                                s_append_asprintf(errbuf, "line %d: sigma for xtalcell are missing", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        if (sscanf(buf, "%lf %lf %lf %lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3], &dbuf[4], &dbuf[5]) < 6) {
                                                s_append_asprintf(errbuf,"line %d: bad xtalcell sigma format", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        if (mp->cell != NULL) {
                                                mp->cell->has_sigma = 1;
@@ -1237,7 +1237,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* a11 a12 a13; a21 a22 a23; a31 a32 a33; t1 t2 t3 */
                                if (sscanf(buf, "%lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2]) < 3) {
                                        s_append_asprintf(errbuf, "line %d: bad symmetry_operation format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i < 3) {
                                        tr[i] = dbuf[0];
@@ -1265,11 +1265,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* b11 b22 b33 b12 b13 b23 [has_sigma] */
                                if ((j = sscanf(buf, "%lf %lf %lf %lf %lf %lf %d", &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3], &dbuf[4], &dbuf[5], &ibuf[0])) < 6) {
                                        s_append_asprintf(errbuf, "line %d: anisotropic thermal parameters cannot be read for atom %d", lineNumber, i + 1);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: too many anisotropic thermal parameters\n", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (dbuf[0] == 0.0 && dbuf[1] == 0.0 && dbuf[2] == 0.0 && dbuf[3] == 0.0 && dbuf[4] == 0.0 && dbuf[5] == 0.0) {
                                        /*  Skip it  */
@@ -1279,16 +1279,16 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                if (j == 7 && ibuf[0] != 0) {
                                        if (ReadLine(buf, sizeof buf, fp, &lineNumber) <= 0) {
                                                s_append_asprintf(errbuf, "line %d: anisotropic thermal parameters sigma missing", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        if (sscanf(buf, "%lf %lf %lf %lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3], &dbuf[4], &dbuf[5]) < 6) {
                                                s_append_asprintf(errbuf, "line %d: anisotropic thermal parameters sigma cannot be read for atom %d", lineNumber, i + 1);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        ap = ATOM_AT_INDEX(mp->atoms, i);
                                        if (ap->aniso == NULL) {
                                                s_append_asprintf(errbuf, "line %d: anisotropic thermal parameters sigma are given while the parameters are not given", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        ap->aniso->has_bsig = 1;
                                        for (j = 0; j < 6; j++)
@@ -1320,7 +1320,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                }
                                if ((j = sscanf(buf, "%d %d %d %d", &ibuf[0], &ibuf[1], &ibuf[2], &ibuf[3])) < 3) {
                                        s_append_asprintf(errbuf, "line %d: bad periodic_box format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (j == 4 && ibuf[3] != 0)
                                        has_sigma = 1;
@@ -1331,11 +1331,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                if (has_sigma) {
                                        if (ReadLine(buf, sizeof buf, fp, &lineNumber) <= 0) {
                                                s_append_asprintf(errbuf, "line %d: sigma for cell parameters are missing", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        if (sscanf(buf, "%lf %lf %lf %lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3], &dbuf[4], &dbuf[5]) < 6) {
                                                s_append_asprintf(errbuf, "line %d: bad periodic_box sigma format", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        if (mp->cell != NULL) {
                                                mp->cell->has_sigma = 1;
@@ -1360,7 +1360,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        break;
                                if (sscanf(buf, "%lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2]) < 3) {
                                        s_append_asprintf(errbuf, "line %d: bad frame_periodic_box format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                vs[i].x = dbuf[0];
                                vs[i].y = dbuf[1];
@@ -1406,7 +1406,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                                        if (k < '0' || k > '9') {
                                                                s_append_asprintf(errbuf, "line %d: too few flags in alchem_flags block", lineNumber + 1);
                                                                free(valp);
-                                                               goto err_exit;
+                                                               goto skip_section;
                                                        }
                                                        ReadLine(buf, sizeof buf, fp, &lineNumber);
                                                        bufp = buf;
@@ -1415,13 +1415,13 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                                                        if (i >= j) {
                                                                                s_append_asprintf(errbuf, "line %d: too many flags in alchem_flags block", lineNumber);
                                                                                free(valp);
-                                                                               goto err_exit;
+                                                                               goto skip_section;
                                                                        }
                                                                        valp[i++] = *bufp - '0';
                                                                } else if (*bufp != ' ' && *bufp != '\t' && *bufp != '\n') {
                                                                        s_append_asprintf(errbuf, "line %d: strange character (0x%02x) in alchem_flags block", lineNumber, (int)*bufp);
                                                                        free(valp);
-                                                                       goto err_exit;
+                                                                       goto skip_section;
                                                                }
                                                                bufp++;
                                                        }
@@ -1503,14 +1503,14 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                if (strcmp(comp, "pressure") == 0) {
                                        if (sscanf(valp, "%lf %lf %lf %lf %lf %lf %lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3], &dbuf[4], &dbuf[5], &dbuf[6], &dbuf[7], &dbuf[8]) < 9) {
                                                s_append_asprintf(errbuf, "line %d: bad format", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        for (i = 0; i < 9; i++)
                                                pressure->apply[i] = dbuf[i];
                                } else if (strcmp(comp, "pressure_cell_flexibility") == 0) {
                                        if (sscanf(valp, "%lf %lf %lf %lf %lf %lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3], &dbuf[4], &dbuf[5], &dbuf[6], &dbuf[7]) < 8) {
                                                s_append_asprintf(errbuf, "line %d: bad format", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        for (i = 0; i < 8; i++)
                                                pressure->cell_flexibility[i] = dbuf[i];
@@ -1533,11 +1533,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* idx vx vy vz */
                                if (sscanf(buf, "%d %lf %lf %lf", &ibuf[0], &dbuf[0], &dbuf[1], &dbuf[2]) < 4) {
                                        s_append_asprintf(errbuf, "line %d: atom velocity cannot be read for atom %d", lineNumber, i + 1);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: too many atom velocity records\n", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                ap = ATOM_AT_INDEX(mp->atoms, i);
                                ap->v.x = dbuf[0];
@@ -1556,11 +1556,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                /* idx fx fy fz */
                                if (sscanf(buf, "%d %lf %lf %lf", &ibuf[0], &dbuf[0], &dbuf[1], &dbuf[2]) < 4) {
                                        s_append_asprintf(errbuf, "line %d: atom force cannot be read for atom %d", lineNumber, i + 1);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: too many atom force records\n", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                ap = ATOM_AT_INDEX(mp->atoms, i);
                                ap->f.x = dbuf[0];
@@ -1586,7 +1586,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                if (j < 0) {
                                        s_append_asprintf(errbuf, "%s", bufp);
                                        free(bufp);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                i += j;
                        }
@@ -1611,7 +1611,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        || (i == 2 && sscanf(buf, "%lf %lf %lf %lf",
                                                                                 &dbuf[4], &dbuf[5], &dbuf[6], &dbuf[7]) < 4)) {
                                        s_append_asprintf(errbuf, "line %d: bad trackball format", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (i == 0)
                                        TrackballSetScale(mp->mview->track, dbuf[0]);
@@ -1722,11 +1722,14 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        continue;
                                if (buf[0] == '\n')
                                        break;
-                               /* sym nprims a_idx */
-                               if (sscanf(buf, "%6s %d %d", cbuf[0], &ibuf[0], &ibuf[1]) < 3) {
+                               /* sym nprims a_idx [add_exp] */
+                i = sscanf(buf, "%6s %d %d %d", cbuf[0], &ibuf[0], &ibuf[1], &ibuf[3]);
+                if (i < 3) {
                                        s_append_asprintf(errbuf, "line %d: the gaussian primitive info cannot be read", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
+                if (i == 3)
+                    ibuf[3] = 0;  /*  Additional exponent (JANPA extension)  */
                                if (strcasecmp(cbuf[0], "S") == 0) {
                                        ibuf[2] = 0;
                                } else if (strcasecmp(cbuf[0], "P") == 0) {
@@ -1747,17 +1750,17 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        ibuf[2] = -4;
                                } else {
                                        s_append_asprintf(errbuf, "line %d: the gaussian primitive type %s is unknown", lineNumber, cbuf[0]);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (ibuf[0] <= 0) {
                                        s_append_asprintf(errbuf, "line %d: the number of primitive (%d) must be positive", lineNumber, ibuf[0]);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (ibuf[1] < 0 || ibuf[1] >= mp->natoms) {
                                        s_append_asprintf(errbuf, "line %d: the atom index (%d) is out of range", lineNumber, ibuf[1]);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
-                               MoleculeAddGaussianOrbitalShell(mp, ibuf[1], ibuf[2], ibuf[0], 0);
+                               MoleculeAddGaussianOrbitalShell(mp, ibuf[1], ibuf[2], ibuf[0], ibuf[3]);
                                i = ibuf[0];
                                while (ReadLine(buf, sizeof buf, fp, &lineNumber) > 0) {
                                        if (buf[0] == '!')
@@ -1766,7 +1769,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                                break;
                                        if (sscanf(buf, "%lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2]) < 3) {
                                                s_append_asprintf(errbuf, "line %d: cannot read gaussian primitive coefficients", lineNumber);
-                                               goto err_exit;
+                                               goto skip_section;
                                        }
                                        MoleculeAddGaussianPrimitiveCoefficients(mp, dbuf[0], dbuf[1], dbuf[2]);
                                        if (--i == 0)
@@ -1784,7 +1787,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        break;
                                if (sscanf(buf, "%6s %d %d", cbuf[0], &ibuf[0], &ibuf[1]) < 3) {
                                        s_append_asprintf(errbuf, "line %d: the MO info cannot be correctly read", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (strcasecmp(cbuf[0], "RHF") == 0) {
                                        ibuf[2] = 1;
@@ -1794,11 +1797,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        ibuf[2] = 0;
                                } else {
                                        s_append_asprintf(errbuf, "line %d: unknown HF type: %s", lineNumber, cbuf[0]);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (ibuf[0] < 0 || ibuf[1] < 0) {
                                        s_append_asprintf(errbuf, "line %d: incorrect number of electrons", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                MoleculeSetMOInfo(mp, ibuf[2], ibuf[0], ibuf[1]);
                        }
@@ -1806,7 +1809,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                } else if (strcmp(buf, "!:mo_coefficients") == 0) {
                        if (mp->bset == NULL || mp->bset->nshells == 0) {
                                s_append_asprintf(errbuf, "line %d: the :gaussian_primitive section must come before :mo_coefficients", lineNumber);
-                               goto err_exit;
+                               goto skip_section;
                        }
                        /*  Count the number of components  */
                        dp = (Double *)malloc(sizeof(Double) * mp->bset->ncomps);
@@ -1818,11 +1821,11 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        break;
                                if (sscanf(buf, "MO %d %lf", &ibuf[0], &dbuf[6]) < 2) {
                                        s_append_asprintf(errbuf, "line %d: cannot read the MO index or energy", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                if (ibuf[0] != i) {
                                        s_append_asprintf(errbuf, "line %d: the MO index (%d) must be in ascending order", lineNumber, ibuf[0]);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                i = 0;
                                while (ReadLine(buf, sizeof buf, fp, &lineNumber) > 0) {
@@ -1844,7 +1847,7 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                i = MoleculeSetMOCoefficients(mp, ibuf[0], dbuf[6], mp->bset->ncomps, dp);
                                if (i != 0) {
                                        s_append_asprintf(errbuf, "line %d: cannot set MO coefficients", lineNumber);
-                                       goto err_exit;
+                                       goto skip_section;
                                }
                                i = ibuf[0] + 1;  /*  For next entry  */
                        }
@@ -1883,14 +1886,14 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                        if (i == 0) {
                                                if (sscanf(buf, "%d %d", &ibuf[0], &ibuf[1]) < 2) {
                                                        s_append_asprintf(errbuf, "line %d: the closed/visible flags cannot be read for graphic object", lineNumber);
-                                                       goto err_exit;
+                                                       goto skip_section;
                                                }
                                                gp->closed = ibuf[0];
                                                gp->visible = ibuf[1];
                                        } else if (i == 1) {
                                                if (sscanf(buf, "%lf %lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2], &dbuf[3]) < 4) {
                                                        s_append_asprintf(errbuf, "line %d: the color cannot be read for graphic object", lineNumber);
-                                                       goto err_exit;
+                                                       goto skip_section;
                                                }
                                                for (j = 0; j < 4; j++)
                                                        gp->rgba[j] = dbuf[j];
@@ -1898,14 +1901,14 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                                j = atoi(buf);
                                                if (j < 0) {
                                                        s_append_asprintf(errbuf, "line %d: the number of control points must be non-negative", lineNumber);
-                                                       goto err_exit;
+                                                       goto skip_section;
                                                }
                                                if (j > 0)
                                                        NewArray(&gp->points, &gp->npoints, sizeof(GLfloat) * 3, j);
                                        } else if (i >= 3 && i < gp->npoints + 3) {
                                                if (sscanf(buf, "%lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2]) < 3) {
                                                        s_append_asprintf(errbuf, "line %d: the control point cannot be read for graphic object", lineNumber);
-                                                       goto err_exit;
+                                                       goto skip_section;
                                                }
                                                j = (i - 3) * 3;
                                                gp->points[j++] = dbuf[0];
@@ -1915,14 +1918,14 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                                j = atoi(buf);
                                                if (j < 0) {
                                                        s_append_asprintf(errbuf, "line %d: the number of normals must be non-negative", lineNumber);
-                                                       goto err_exit;
+                                                       goto skip_section;
                                                }
                                                if (j > 0)
                                                        NewArray(&gp->normals, &gp->nnormals, sizeof(GLfloat) * 3, j);
                                        } else if (i >= gp->npoints + 4 && i < gp->npoints + gp->nnormals + 4) {
                                                if (sscanf(buf, "%lf %lf %lf", &dbuf[0], &dbuf[1], &dbuf[2]) < 3) {
                                                        s_append_asprintf(errbuf, "line %d: the normal vector cannot be read for graphic object", lineNumber);
-                                                       goto err_exit;
+                                                       goto skip_section;
                                                }
                                                j = (i - gp->npoints - 4) * 3;
                                                gp->normals[j++] = dbuf[0];
@@ -1938,6 +1941,34 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                goto redo;
                        }
                        continue;
+        } else if (strcmp(buf, "!:nbo") == 0) {
+            Int stringLen;
+            char *stringBuf, *returnString;
+            i = strlen(buf) + 1;  /*  Including \n  */
+            NewArray(&stringBuf, &stringLen, sizeof(char), i + 1);
+            strcpy(stringBuf, buf);
+            strcat(stringBuf, "\n");
+            k = lineNumber;
+            while (ReadLine(buf, sizeof buf, fp, &lineNumber) > 0) {
+                /*  The comment lines are _not_ skipped  */
+                if (buf[0] == '\n')
+                    break;
+                j = strlen(buf);
+                AssignArray(&stringBuf, &stringLen, sizeof(char), i + j, NULL);
+                strncpy(stringBuf + i, buf, j);
+                i += j;
+            }
+            if (MolActionCreateAndPerform(mp, SCRIPT_ACTION("si;s"),
+                                          "proc { |s,i| mbsfstring2nbo(s,i) }",
+                                          stringBuf, k, &returnString) != 0) {
+                s_append_asprintf(errbuf, "line %d: cannot call mbsfstring2nbo at line ", lineNumber);
+                goto skip_section;
+            } else if (returnString[0] != 0) {
+                s_append_asprintf(errbuf, "%s", returnString);
+                goto skip_section;
+            }
+            free(stringBuf);
+            continue;
                } else if (strncmp(buf, "!:@", 3) == 0) {
                        /*  Plug-in implemented in the ruby world  */
                        Int stringLen;
@@ -1959,15 +1990,16 @@ MoleculeLoadMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                                                                  "proc { |i| loadmbsf_plugin(i) rescue \"line #{i}: #{$i.to_s}\" }",
                                                                                  stringBuf, k, &returnString) != 0) {
                                s_append_asprintf(errbuf, "line %d: cannot invoke Ruby plugin", lineNumber);
-                               goto err_exit;
+                               goto skip_section;
                        } else if (returnString[0] != 0) {
                                s_append_asprintf(errbuf, "%s", returnString);
-                               goto err_exit;
+                               goto skip_section;
                        }
                        free(stringBuf);
                        continue;
                }
                /*  Unknown sections are silently ignored  */
+    skip_section:;
        }
 
        MoleculeCleanUpResidueTable(mp);
@@ -2778,9 +2810,10 @@ MoleculeAddGaussianPrimitiveCoefficients(Molecule *mol, Double exponent, Double
 }
 
 /*  Get the shell information from the component index  */
-/*  The outLabel must have space for at least 23 non-Null characters  */
+/*  The outLabel must have space for at least 31 non-Null characters  */
+/*  See also: sub load_janpa_log in loadsave.rb  */
 int
-MoleculeGetGaussianComponentInfo(Molecule *mol, Int comp_idx, Int *outAtomIdx, char *outLabel, Int *outShellIdx)
+MoleculeGetGaussianComponentInfo(Molecule *mol, Int comp_idx, Int *outAtomIdx, char outLabel[32], Int *outShellIdx)
 {
        BasisSet *bset;
        ShellInfo *shellp;
@@ -2800,8 +2833,8 @@ MoleculeGetGaussianComponentInfo(Molecule *mol, Int comp_idx, Int *outAtomIdx, c
                        static const char *type_f = "xxxyyyzzzxxyxxzxyyyyzxzzyzzxyz";
                        static const char *type_f7[] = {"z3-zr2", "xz2-xr2", "yz2-yr2", "x2z-y2z", "xyz", "x3-xy2", "x2y-y3"};
                        static const char *type_g[] = {"x4", "y4", "z4", "x3y", "x3z", "xy3", "y3z", "xz3", "yz3", "x2y2", "x2z2", "y2z2", "x2yz", "xy2z", "xyz2"};
-                       static const char *type_g9[] = {"z4-z2r2+r4", "xz3-xzr2", "yz3-yzr2", "(x2-y2)(z2-r2)", "xyz2-xyr2", "x3z-xy2z", "x2yz-y3z", "x4-x2y2+y4", "x3y-xy3"};
-                       *outAtomIdx = shellp->a_idx;
+                       static const char *type_g9[] = {"z4-z2r2+r4", "xz3-xzr2", "yz3-yzr2", "x2z2-y2z2", "xyz2-xyr2", "x3z-xy2z", "x2yz-y3z", "x4-x2y2+y4", "x3y-xy3"};
+            *outAtomIdx = shellp->a_idx;
                        *outShellIdx = si;
                        switch (shellp->sym) {
                                case kGTOType_S:
@@ -2828,7 +2861,8 @@ MoleculeGetGaussianComponentInfo(Molecule *mol, Int comp_idx, Int *outAtomIdx, c
                                        break;
                                case kGTOType_D5:
                                        outLabel[0] = 'D';
-                                       strcpy(outLabel + 1, type_d5[comp_idx]);
+                                       strncpy(outLabel + 1, type_d5[comp_idx], 30);
+                    outLabel[31] = 0;
                                        break;
                                case kGTOType_F:
                                        outLabel[0] = 'F';
@@ -2837,19 +2871,30 @@ MoleculeGetGaussianComponentInfo(Molecule *mol, Int comp_idx, Int *outAtomIdx, c
                                        break;
                                case kGTOType_F7:
                                        outLabel[0] = 'F';
-                                       strcpy(outLabel + 1, type_f7[comp_idx]);
+                                       strncpy(outLabel + 1, type_f7[comp_idx], 30);
+                    outLabel[31] = 0;
                                        break;
                                case kGTOType_G:
                                        outLabel[0] = 'G';
-                                       strcpy(outLabel + 1, type_g[comp_idx]);
+                                       strncpy(outLabel + 1, type_g[comp_idx], 30);
+                    outLabel[31] = 0;
                                        break;
                                case kGTOType_G9:
                                        outLabel[0] = 'G';
-                                       strcpy(outLabel + 1, type_g9[comp_idx]);
+                                       strncpy(outLabel + 1, type_g9[comp_idx], 30);
+                    outLabel[31] = 0;
                                        break;
                                default:
                                        return -3;  /*  Unsupported orbital type (internal error) */
                        }
+            if (shellp->add_exp > 0) {
+                /*  Additional exponent (JANPA extension): like "s*r2", "dxx-yy*r4", etc. */
+                int len = strlen(outLabel);
+                if (len < 28) {
+                    snprintf(outLabel + len, 32 - len, "*r%d", shellp->add_exp);
+                }
+                outLabel[31] = 0;
+            }
                        return 0;
                }
        }
@@ -4770,7 +4815,7 @@ MoleculeWriteToMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                ShellInfo *sp;
                PrimInfo *pp;
                fprintf(fp, "!:gaussian_primitives\n");
-               fprintf(fp, "! sym nprims a_idx; A C Csp\n");
+               fprintf(fp, "! sym nprims a_idx [add_exp]; A C Csp\n");
                for (i = 0, sp = mp->bset->shells; i < mp->bset->nshells; i++, sp++) {
                        switch (sp->sym) {
                                case kGTOType_S:  p = "S";  break;
@@ -4784,7 +4829,10 @@ MoleculeWriteToMbsfFile(Molecule *mp, const char *fname, char **errbuf)
                                case kGTOType_G9: p = "G9"; break;
                                default: snprintf(bufs[0], 8, "X%d", sp->sym); p = bufs[0]; break;
                        }
-                       fprintf(fp, "%s %d %d\n", p, sp->nprim, sp->a_idx);
+            if (sp->add_exp == 0)
+                fprintf(fp, "%s %d %d\n", p, sp->nprim, sp->a_idx);
+            else
+                fprintf(fp, "%s %d %d %d\n", p, sp->nprim, sp->a_idx, sp->add_exp);
                        pp = mp->bset->priminfos + sp->p_idx;
                        for (j = 0; j < sp->nprim; j++, pp++) {
                                fprintf(fp, "%.18g %.18g %.18g\n", pp->A, pp->C, pp->Csp);
@@ -4843,10 +4891,20 @@ MoleculeWriteToMbsfFile(Molecule *mp, const char *fname, char **errbuf)
        /*  Plug-in in the Ruby world  */
        {
                char *outMessage;
+        /*  Save NBO information  */
+        if (MolActionCreateAndPerform(mp, SCRIPT_ACTION(";s"),
+                                      "proc { nbo2msbfstring rescue \"Plug-in error: #{$!.to_s}\" }", &outMessage) == 0) {
+            if (strncmp(outMessage, "Plug-in error", 13) == 0) {
+                s_append_asprintf(errbuf, "%s", outMessage);
+            }
+            fputs(outMessage, fp);
+            free(outMessage);
+        }
+        /*  Other Plug-in  */
                if (MolActionCreateAndPerform(mp, SCRIPT_ACTION(";s"),
                                                                          "proc { savembsf_plugin rescue \"Plug-in error: #{$!.to_s}\" }", &outMessage) == 0) {
                        if (outMessage[0] != 0) {
-                               if (strncmp(outMessage, "Plug-in", 7) == 0) {
+                               if (strncmp(outMessage, "Plug-in error", 13) == 0) {
                                        s_append_asprintf(errbuf, "%s", outMessage);
                                } else {
                                        fprintf(fp, "%s\n", outMessage);

diff --git a/MolLib/Molecule.h b/MolLib/Molecule.h
index b7da244..3edd403 100755 (executable)
--- a/MolLib/Molecule.h
+++ b/MolLib/Molecule.h
@@ -414,7 +414,7 @@ void MoleculeExchange(Molecule *mp1, Molecule *mp2);
 
 int MoleculeAddGaussianOrbitalShell(Molecule *mol, Int a_idx, Int sym, Int nprims, Int add_exp);
 int MoleculeAddGaussianPrimitiveCoefficients(Molecule *mol, Double exponent, Double contraction, Double contraction_sp);
-int MoleculeGetGaussianComponentInfo(Molecule *mol, Int comp_idx, Int *outAtomIdx, char *outLabel, Int *outShellIdx);
+int MoleculeGetGaussianComponentInfo(Molecule *mol, Int comp_idx, Int *outAtomIdx, char outLabel[32], Int *outShellIdx);
 int MoleculeSetMOCoefficients(Molecule *mol, Int idx, Double energy, Int ncomps, Double *coeffs);
 int MoleculeGetMOCoefficients(Molecule *mol, Int idx, Double *energy, Int *ncoeffs, Double **coeffs);
 int MoleculeSetMOInfo(Molecule *mol, Int rflag, Int ne_alpha, Int ne_beta);

diff --git a/Scripts/loadsave.rb b/Scripts/loadsave.rb
index 738beb2..fc03f43 100755 (executable)
--- a/Scripts/loadsave.rb
+++ b/Scripts/loadsave.rb
@@ -817,6 +817,7 @@ class Molecule
   #  and load from it (i.e. use the basis set converted by molden2molden)
   def sub_load_janpa_log(inppath)
     begin
+      #  See also: MoleculeGetGaussianComponentInfo() in Molecule.c
       m2name_p = {0=>"x", 1=>"y", -1=>"z"}
       m2name_d = {0=>"zz-rr", 1=>"xz", -1=>"yz", 2=>"xx-yy", -2=>"xy"}
       m2name_f = {0=>"z3-zr2", 1=>"xz2-xr2", -1=>"yz2-yr2", 2=>"x2z-y2z", -2=>"xyz", 3=>"x3-xy2", -3=>"x2y-y3"}
@@ -1208,6 +1209,119 @@ class Molecule
     end
   end
 
+  #  Convert @nbo info to an msbf string (multiline)
+  #  !:nbo
+  #  [XXX] (NAO, LHO, etc.)
+  #  nn (number of components)
+  #  (nao_labels)*nn, one per line
+  #  XXX n
+  #  (%.18g)*nn, at most 6 per line
+  def nbo2msbfstring
+    unless @nbo
+      return ""
+    end
+    keys = @nbo.keys.grep(/AO\/\w+/)
+    s = "!:nbo\n"
+    keys.each { |k|
+      k =~ /AO\/(\w+)/
+      key = $1
+      labels = @nbo[key + "_L"]
+      m = @nbo[k]
+      nc = m.column_size
+      s += "[#{key}]\n#{nc}\n"
+      nc.times { |i|
+        l = (labels ? labels[i] : "")
+        s += "#{key} #{i+1} #{l}\n"
+        nc.times { |j|
+          s += sprintf("%.18g%s", m[i, j], ((j == nc - 1 || j % 6 == 5) ? "\n" : " "))
+        }
+      }
+    }
+    s += "\n"
+    s
+  end
+
+  #  Read @nbo info from a multiline string and set to @nbo
+  def mbsfstring2nbo(s, first_lineno)
+    h = Hash.new
+    lineno = first_lineno - 1
+    errmsg = "Error reading NBO section: "
+    key = nil
+    nc = nil
+    labels = nil
+    mo_matrix = nil
+    mo = nil
+    s.each_line { |ln|
+      lineno += 1
+      next if lineno == first_lineno
+      ln.chomp!
+      if key == nil
+        if ln =~ /\[(\w+)\]/
+          key = $1
+        else
+          return errmsg + "keyword (like NBO, NHO, ...) is expected at line #{lineno}"
+        end
+        next
+      end
+      if nc == nil
+        nc = ln.to_i
+        labels = nil
+        mo_matrix = []
+        mo = []
+        next
+      end
+      if ln[0, key.length] == key
+        if mo == nil
+          return errmsg + "number of components is missing"
+        end
+        if mo.length > 0
+          return errmsg + "too few coefficients at line #{lineno}"
+        end
+        ln =~ /^(\w+) +(\d+) *(.*)$/
+        l = $3
+        if l != ""
+          labels ||= []
+          labels[mo_matrix.length] = l.strip
+        end
+        next
+      end
+      m = ln.split
+      begin
+        m = m.map { |c| Float(c) }
+      rescue
+        return errmsg + "cannot convert to number at line #{lineno}"
+      end
+      mo += m
+      if mo.length > nc
+        return errmsg + "too many coefficients at line #{lineno}"
+      end
+      if mo.length == nc
+        mo_matrix.push(mo)
+        mo = []
+        if mo_matrix.length == nc
+          #  All components are correctly read
+          if labels
+            #  Set the label if not specified
+            nc.times { |i|
+              if !labels[i] || labels[i] == ""
+                labels[i] = "#{key}#{i+1}"
+              end
+            }
+            h["#{key}_L"] = labels
+          end
+          h["AO/#{key}"] = LAMatrix.new(mo_matrix)
+          mo = nil
+          mo_matrix = nil
+          labels = nil
+          key = nil
+          nc = nil
+        end
+      end
+    }  #  end each_line
+    @nbo = h
+    return ""
+  end
+  
   def loadout(filename)
   retval = false
   fp = open(filename, "rb")

diff --git a/wxSources/MyApp.cpp b/wxSources/MyApp.cpp
index ab495a9..1cdab83 100755 (executable)
--- a/wxSources/MyApp.cpp
+++ b/wxSources/MyApp.cpp
@@ -1465,7 +1465,7 @@ MyApp::CallSubProcess(const char **argv, const char *procname, int (*callback)(v
         pid = ::wxExecute(argv[0], flag, m_process);
     } else {
         //  Array of arguments
-        pid = ::wxExecute(argv, flag, m_process);
+        pid = ::wxExecuteArgv(argv, flag, m_process);
     }
        if (pid == 0) {
         if (progress_panel)
@@ -2411,7 +2411,7 @@ void MyAppCallback_endUndoGrouping(void)
 int MyAppCallback_callSubProcess(const char **argv, const char *procname, int (*callback)(void *), void *callback_data, FILE *output, FILE *errout, int *exitstatus_p, int *pid_p)
 {
     if (!gUseGUI)
-        return ::wxExecute(argv, wxEXEC_SYNC | wxEXEC_HIDE_CONSOLE);
+        return ::wxExecuteArgv(argv, wxEXEC_SYNC | wxEXEC_HIDE_CONSOLE, NULL);
     else
         return wxGetApp().CallSubProcess(argv, procname, callback, callback_data, output, errout, exitstatus_p, pid_p);
 }

diff --git a/wxSources/MyApp.h b/wxSources/MyApp.h
index df27e1e..3052287 100755 (executable)
--- a/wxSources/MyApp.h
+++ b/wxSources/MyApp.h
@@ -175,6 +175,11 @@ protected:
     wxMemoryBuffer m_stdin;
 };
 
+#if wxCHECK_VERSION(3,1,0)
+#define wxExecuteArgv(_argv, _flags, _process) wxExecute(_argv, _flags, _process)
+#else
+#define wxExecuteArgv(_argv, _flags, _process) wxExecute((char **)(_argv), _flags, _process)
+#endif
 
 // Define a new application
 class MyApp: public wxApp

diff --git a/wxSources/MyDocument.cpp b/wxSources/MyDocument.cpp
index 1bbc49f..b4ad7b2 100755 (executable)
--- a/wxSources/MyDocument.cpp
+++ b/wxSources/MyDocument.cpp
@@ -230,7 +230,10 @@ MyDocument::DoOpenDocument(const wxString& file)
                return false;
        }
        
-       /*  Does this document have multiple representation of molecules?  */
+  if (gLoadSaveErrorMessage != NULL)
+    MyAppCallback_showScriptMessage("On loading %s:\n%s\n", p, gLoadSaveErrorMessage);
+
+  /*  Does this document have multiple representation of molecules?  */
        if (MolActionCreateAndPerform(newmol, SCRIPT_ACTION(";i"), "lambda { @aux_mols ? @aux_mols.count : 0 }", &len) == 0 && len > 0) {
                wxCommandEvent myEvent(MyDocumentEvent, MyDocumentEvent_openAuxiliaryDocuments);
                wxPostEvent(this, myEvent);
@@ -1151,7 +1154,7 @@ MyDocument::RunSubProcess(const char **argv, int (*callback)(Molecule *, int), i
     subProcessPID = ::wxExecute(argv[0], wxEXEC_ASYNC | wxEXEC_MAKE_GROUP_LEADER, subProcess);
   } else {
     // Array of arguments
-    subProcessPID = ::wxExecute(argv, wxEXEC_ASYNC | wxEXEC_MAKE_GROUP_LEADER, subProcess);
+    subProcessPID = ::wxExecuteArgv(argv, wxEXEC_ASYNC | wxEXEC_MAKE_GROUP_LEADER, subProcess);
   }
        if (subProcessPID == 0) {
                subProcess->Detach();