The MM/MD engine was not aware of modification of coordinates via Ruby scripts. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@28 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/MolLib/MD/MDCore.c b/MolLib/MD/MDCore.c
index dd2ebe9..cf00d64 100644 (file)
--- a/MolLib/MD/MDCore.c
+++ b/MolLib/MD/MDCore.c
@@ -2630,6 +2630,7 @@ md_copy_coordinates_to_internal(MDArena *arena)
        }
        if (arena->mol->cell != NULL && arena->xmol->cell != NULL)
                memmove(arena->mol->cell, arena->xmol->cell, sizeof(XtalCell));
+       arena->xmol->needsMDCopyCoordinates = 0;
        return 0;
 }
 
@@ -2657,7 +2658,10 @@ md_main(MDArena *arena, int minimize)
                        snprintf(arena->errmsg, sizeof(arena->errmsg), "%s", msg);
                        return 1;
                }
-               /*  Copy coordinates  */
+               arena->xmol->needsMDCopyCoordinates = 1;  /*  Coordinates will be copied below  */
+       }
+       
+       if (arena->xmol->needsMDCopyCoordinates) {
                MoleculeLock(arena->xmol);
                retval = md_copy_coordinates_to_internal(arena);
                MoleculeUnlock(arena->xmol);

diff --git a/MolLib/MolAction.c b/MolLib/MolAction.c
index 6ddc272..994b89c 100644 (file)
--- a/MolLib/MolAction.c
+++ b/MolLib/MolAction.c
@@ -1262,6 +1262,7 @@ MolActionPerform(Molecule *mol, MolAction *action)
                        free(vp2);
                        IntGroupRelease(ig2);
                }
+               mol->needsMDCopyCoordinates = 1;
        }
        
        if (needsRebuildMDArena) {

diff --git a/MolLib/Molecule.c b/MolLib/Molecule.c
index d5a0723..7ea55d2 100755 (executable)
--- a/MolLib/Molecule.c
+++ b/MolLib/Molecule.c
@@ -4989,6 +4989,7 @@ MoleculeAmendBySymmetry(Molecule *mp, IntGroup *group, IntGroup **groupout, Vect
                ap->r = nr;
                count++;
        }
+       mp->needsMDCopyCoordinates = 1;
        __MoleculeUnlock(mp);
        if (groupout != NULL) {
                if (count == 0) {
@@ -7009,6 +7010,7 @@ MoleculeTransform(Molecule *mp, Transform tr, IntGroup *group)
                        continue;
                TransformVec(&ap->r, tr, &ap->r);
        }
+       mp->needsMDCopyCoordinates = 1;
        __MoleculeUnlock(mp);
        sMoleculeNotifyChangeAppearance(mp);
 }
@@ -7026,6 +7028,7 @@ MoleculeMove(Molecule *mp, Transform tr, IntGroup *group)
                        continue;
                TransformVec(&ap->r, tr, &ap->r);
        }
+       mp->needsMDCopyCoordinates = 1;
        __MoleculeUnlock(mp);
        sMoleculeNotifyChangeAppearance(mp);
 }
@@ -7043,6 +7046,7 @@ MoleculeTranslate(Molecule *mp, const Vector *vp, IntGroup *group)
                        continue;
                VecInc(ap->r, *vp);
        }
+       mp->needsMDCopyCoordinates = 1;
        __MoleculeUnlock(mp);
        sMoleculeNotifyChangeAppearance(mp);
 }
@@ -7073,6 +7077,7 @@ MoleculeRotate(Molecule *mp, const Vector *axis, Double angle, const Vector *cen
                        continue;
                TransformVec(&ap->r, tr, &ap->r);
        }
+       mp->needsMDCopyCoordinates = 1;
        __MoleculeUnlock(mp);
        sMoleculeNotifyChangeAppearance(mp);
 }
@@ -7094,6 +7099,7 @@ MoleculeReaxis(Molecule *mp, const Vector *xaxis, const Vector *yaxis, const Vec
                v.z = VecDot(ap->r, *zaxis);
                ap->r = v;
        }
+       mp->needsMDCopyCoordinates = 1;
        __MoleculeUnlock(mp);
        sMoleculeNotifyChangeAppearance(mp);
 }
@@ -8081,7 +8087,7 @@ MoleculeSelectFrame(Molecule *mp, int frame, int copyback)
        if (mp->cell != NULL && mp->frame_cells != NULL) {
                MoleculeSetPeriodicBox(mp, &mp->frame_cells[frame * 4], &mp->frame_cells[frame * 4 + 1], &mp->frame_cells[frame * 4 + 2], &mp->frame_cells[frame * 4 + 3], mp->cell->flags);
        }
-
+       mp->needsMDCopyCoordinates = 1;
        __MoleculeUnlock(mp);
        if (ok) {
                mp->cframe = frame;

diff --git a/MolLib/Molecule.h b/MolLib/Molecule.h
index 14fb772..784eb8a 100755 (executable)
--- a/MolLib/Molecule.h
+++ b/MolLib/Molecule.h
@@ -282,6 +282,9 @@ typedef struct Molecule {
        /*  Flag to request rebuilding MD internal information  */
        Byte   needsMDRebuild;
        
+       /*  Flag to request copying coordinates to MD arena  */
+       Byte   needsMDCopyCoordinates;
+
        /*  Prohibit modification of the topology (to avoid interfering MD) */
        Byte   noModifyTopology;
        

diff --git a/MolLib/Ruby_bind/ruby_bind.c b/MolLib/Ruby_bind/ruby_bind.c
index d8c1fa1..469d31e 100644 (file)
--- a/MolLib/Ruby_bind/ruby_bind.c
+++ b/MolLib/Ruby_bind/ruby_bind.c
@@ -3094,6 +3094,14 @@ s_AtomFromValue(VALUE self)
        return ap;
 }
 
+static Atom *
+s_AtomAndMoleculeFromValue(VALUE self, Molecule **mpp)
+{
+       Atom *ap;
+       s_AtomIndexFromValue(self, &ap, mpp);
+       return ap;
+}
+
 static void
 s_NotifyModificationForAtomRef(VALUE self)
 {
@@ -3306,35 +3314,42 @@ static VALUE s_AtomRef_SetName(VALUE self, VALUE val) {
 }
 
 static VALUE s_AtomRef_SetAtomType(VALUE self, VALUE val) {
+       Molecule *mp;
        char *p = StringValuePtr(val);
        VALUE oval = s_AtomRef_GetAtomType(self);
        int type = (p[0] == 0 ? 0 : AtomTypeEncodeToUInt(p));
        if (type != 0 && type < kAtomTypeMinimum)
                rb_raise(rb_eMolbyError, "Invalid atom type '%s'", p);
-       s_AtomFromValue(self)->type = type;
+       s_AtomAndMoleculeFromValue(self, &mp)->type = type;
+       mp->needsMDRebuild = 1;
        s_RegisterUndoForAtomAttrChange(self, s_AtomTypeSym, val, oval);
        return val;
 }
 
 static VALUE s_AtomRef_SetCharge(VALUE self, VALUE val) {
+       Molecule *mp;
        VALUE oval = s_AtomRef_GetCharge(self);
        val = rb_Float(val);
-       s_AtomFromValue(self)->charge = NUM2DBL(val);
+       s_AtomAndMoleculeFromValue(self, &mp)->charge = NUM2DBL(val);
+       mp->needsMDRebuild = 1;
        s_RegisterUndoForAtomAttrChange(self, s_ChargeSym, val, oval);
        return val;
 }
 
 static VALUE s_AtomRef_SetWeight(VALUE self, VALUE val) {
+       Molecule *mp;
        VALUE oval = s_AtomRef_GetWeight(self);
        val = rb_Float(val);
-       s_AtomFromValue(self)->weight = NUM2DBL(val);
+       s_AtomAndMoleculeFromValue(self, &mp)->weight = NUM2DBL(val);
+       mp->needsMDRebuild = 1;
        s_RegisterUndoForAtomAttrChange(self, s_WeightSym, val, oval);
        return val;
 }
 
 static VALUE s_AtomRef_SetElement(VALUE self, VALUE val) {
        Double w;
-       Atom *ap = s_AtomFromValue(self);
+       Molecule *mp;
+       Atom *ap = s_AtomAndMoleculeFromValue(self, &mp);
        char *p = StringValuePtr(val);
        VALUE oval = s_AtomRef_GetElement(self);
        ap->atomicNumber = ElementToInt(p);
@@ -3342,12 +3357,14 @@ static VALUE s_AtomRef_SetElement(VALUE self, VALUE val) {
        if ((w = WeightForAtomicNumber(ap->atomicNumber)) > 0.0)
                ap->weight = w;
        s_RegisterUndoForAtomAttrChange(self, s_ElementSym, val, oval);
+       mp->needsMDRebuild = 1;
        return val;
 }
 
 static VALUE s_AtomRef_SetAtomicNumber(VALUE self, VALUE val) {
        Double w;
-       Atom *ap = s_AtomFromValue(self);
+       Molecule *mp;
+       Atom *ap = s_AtomAndMoleculeFromValue(self, &mp);
        VALUE oval = s_AtomRef_GetAtomicNumber(self);
        val = rb_Integer(val);
        ap->atomicNumber = NUM2INT(val);
@@ -3355,6 +3372,7 @@ static VALUE s_AtomRef_SetAtomicNumber(VALUE self, VALUE val) {
        if ((w = WeightForAtomicNumber(ap->atomicNumber)) > 0.0)
                ap->weight = w;
        s_RegisterUndoForAtomAttrChange(self, s_AtomicNumberSym, val, oval);
+       mp->needsMDRebuild = 1;
        return val;
 }
 
@@ -3365,40 +3383,48 @@ static VALUE s_AtomRef_SetConnects(VALUE self, VALUE val) {
 
 static VALUE s_AtomRef_SetR(VALUE self, VALUE val) {
        Vector v;
+       Molecule *mp;
        VALUE oval = s_AtomRef_GetR(self);
        VectorFromValue(val, &v);
-       s_AtomFromValue(self)->r = v;
+       s_AtomAndMoleculeFromValue(self, &mp)->r = v;
        s_RegisterUndoForAtomAttrChange(self, s_RSym, val, oval);
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
 static VALUE s_AtomRef_SetX(VALUE self, VALUE val) {
        Double f;
+       Molecule *mp;
        VALUE oval = s_AtomRef_GetX(self);
        val = rb_Float(val);
        f = NUM2DBL(val);
-       s_AtomFromValue(self)->r.x = f;
+       s_AtomAndMoleculeFromValue(self, &mp)->r.x = f;
        s_RegisterUndoForAtomAttrChange(self, s_XSym, val, oval);
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
 static VALUE s_AtomRef_SetY(VALUE self, VALUE val) {
        Double f;
+       Molecule *mp;
        VALUE oval = s_AtomRef_GetY(self);
        val = rb_Float(val);
        f = NUM2DBL(val);
-       s_AtomFromValue(self)->r.y = f;
+       s_AtomAndMoleculeFromValue(self, &mp)->r.y = f;
        s_RegisterUndoForAtomAttrChange(self, s_YSym, val, oval);
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
 static VALUE s_AtomRef_SetZ(VALUE self, VALUE val) {
        Double f;
+       Molecule *mp;
        VALUE oval = s_AtomRef_GetZ(self);
        val = rb_Float(val);
        f = NUM2DBL(val);
-       s_AtomFromValue(self)->r.z = f;
+       s_AtomAndMoleculeFromValue(self, &mp)->r.z = f;
        s_RegisterUndoForAtomAttrChange(self, s_ZSym, val, oval);
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
@@ -3413,6 +3439,7 @@ static VALUE s_AtomRef_SetFractionalR(VALUE self, VALUE val) {
                TransformVec(&v, mp->cell->tr, &v);
        ap->r = v;
        s_RegisterUndoForAtomAttrChange(self, s_RSym, Qnil, ValueFromVector(&ov));
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
@@ -3432,6 +3459,7 @@ static VALUE s_AtomRef_SetFractionalX(VALUE self, VALUE val) {
        } else v.x = f;
        ap->r = v;
        s_RegisterUndoForAtomAttrChange(self, s_RSym, Qnil, ValueFromVector(&ov));
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
@@ -3451,6 +3479,7 @@ static VALUE s_AtomRef_SetFractionalY(VALUE self, VALUE val) {
        } else v.y = f;
        ap->r = v;
        s_RegisterUndoForAtomAttrChange(self, s_RSym, Qnil, ValueFromVector(&ov));
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
@@ -3470,6 +3499,7 @@ static VALUE s_AtomRef_SetFractionalZ(VALUE self, VALUE val) {
        } else v.z = f;
        ap->r = v;
        s_RegisterUndoForAtomAttrChange(self, s_RSym, Qnil, ValueFromVector(&ov));
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
@@ -3483,15 +3513,18 @@ static VALUE s_AtomRef_SetV(VALUE self, VALUE val) {
        s_AtomIndexFromValue(self, &ap, &mp);
        ap->v = v;
        s_RegisterUndoForAtomAttrChange(self, s_VSym, val, oval);
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
 static VALUE s_AtomRef_SetF(VALUE self, VALUE val) {
        Vector v;
+       Molecule *mp;
        VALUE oval = s_AtomRef_GetF(self);
        VectorFromValue(val, &v);
-       s_AtomFromValue(self)->f = v;
+       s_AtomAndMoleculeFromValue(self, &mp)->f = v;
        s_RegisterUndoForAtomAttrChange(self, s_FSym, val, oval);
+       mp->needsMDCopyCoordinates = 1;
        return val;
 }
 
@@ -3541,19 +3574,23 @@ static VALUE s_AtomRef_SetIntCharge(VALUE self, VALUE val) {
 }
 
 static VALUE s_AtomRef_SetFixForce(VALUE self, VALUE val) {
+       Molecule *mp;
        VALUE oval = s_AtomRef_GetFixForce(self);
        val = rb_Float(val);
-       s_AtomFromValue(self)->fix_force = NUM2DBL(val) * KCAL2INTERNAL;
+       s_AtomAndMoleculeFromValue(self, &mp)->fix_force = NUM2DBL(val) * KCAL2INTERNAL;
        s_RegisterUndoForAtomAttrChange(self, s_FixForceSym, val, oval);
+       mp->needsMDRebuild = 1;
        return val;
 }
 
 static VALUE s_AtomRef_SetFixPos(VALUE self, VALUE val) {
        Vector v;
+       Molecule *mp;
        VALUE oval = s_AtomRef_GetFixPos(self);
        VectorFromValue(val, &v);
-       s_AtomFromValue(self)->fix_pos = v;
+       s_AtomAndMoleculeFromValue(self, &mp)->fix_pos = v;
        s_RegisterUndoForAtomAttrChange(self, s_FixPosSym, val, oval);
+       mp->needsMDRebuild = 1;
        return val;
 }
 
@@ -5937,7 +5974,8 @@ s_Molecule_InsertFrames(int argc, VALUE *argv, VALUE self)
        VALUE val, coords, cells;
     Molecule *mol;
        IntGroup *ig;
-       int count, ival, i, j, len, nframes;
+       int count, ival, i, j, len, len_c, len2, nframes;
+       VALUE *ptr, *ptr2;
        Vector *vp, *vp2;
     Data_Get_Struct(self, Molecule, mol);
        rb_scan_args(argc, argv, "12", &val, &coords, &cells);
@@ -5951,28 +5989,26 @@ s_Molecule_InsertFrames(int argc, VALUE *argv, VALUE self)
                        rb_raise(rb_eTypeError, "the unit cell is not defined but the cell axes are given");
                if (TYPE(cells) != T_ARRAY)
                        rb_raise(rb_eTypeError, "the cell axes should be given as an array of Vector3D");
-               if (len != RARRAY_LEN(coords))
-                       rb_raise(rb_eTypeError, "the number of entries for coordinates and cell axes does not match");
-       }
+               len_c = RARRAY_LEN(cells);
+       } else len_c = 0;
+       count = (len > len_c ? len : len_c);  /*  May be zero; will be updated later  */
        nframes = MoleculeGetNumberOfFrames(mol);
        if (val == Qnil) {
-               ig = IntGroupNewWithPoints(nframes, (len > 0 ? len : 1), -1);
+               ig = IntGroupNewWithPoints(nframes, (count > 0 ? count : 1), -1);
                val = ValueFromIntGroup(ig);
        } else {
                ig = IntGroupFromValue(val);
        }
-       count = IntGroupGetCount(ig);
+       count = IntGroupGetCount(ig);  /*  Count is updated here  */
        vp = ALLOC_N(Vector, mol->natoms * count);
-       if (cells != Qnil && len > 0)
+       if (cells != Qnil)
                vp2 = ALLOC_N(Vector, 4 * count);
        else vp2 = NULL;
        if (len > 0) {
-               VALUE *ptr, *ptr2;
-               int j, len2;
                if (len < count)
                        rb_raise(rb_eMolbyError, "the coordinates should contain no less than %d arrays (for frames)", count);
                ptr = RARRAY_PTR(coords);
-               for (i = 0; i < len; i++) {
+               for (i = 0; i < count; i++) {
                        if (TYPE(ptr[i]) != T_ARRAY)
                                rb_raise(rb_eTypeError, "the coordinate array contains non-array object at index %d", i);
                        len2 = RARRAY_LEN(ptr[i]);
@@ -5982,19 +6018,6 @@ s_Molecule_InsertFrames(int argc, VALUE *argv, VALUE self)
                        for (j = 0; j < mol->natoms; j++)
                                VectorFromValue(ptr2[j], &vp[i * mol->natoms + j]);
                }
-               if (vp2 != NULL) {
-                       ptr = RARRAY_PTR(cells);
-                       for (i = 0; i < len; i++) {
-                               if (TYPE(ptr[i]) != T_ARRAY)
-                                       rb_raise(rb_eTypeError, "the cell parameter array contains non-array object at index %d", i);
-                               len2 = RARRAY_LEN(ptr[i]);
-                               if (len2 < 4)
-                                       rb_raise(rb_eMolbyError, "the cell parameter should contain 4 vectors");
-                               ptr2 = RARRAY_PTR(ptr[i]);
-                               for (j = 0; j < 4; j++)
-                                       VectorFromValue(ptr2[j], &vp2[i * 4 + j]);
-                       }
-               }
        } else {
                Atom *ap;
                for (i = 0; i < count; i++) {
@@ -6003,6 +6026,21 @@ s_Molecule_InsertFrames(int argc, VALUE *argv, VALUE self)
                        }
                }
        }
+       if (len_c > 0) {
+               if (len_c < count)
+                       rb_raise(rb_eMolbyError, "the cell vectors should contain no less than %d arrays (for frames)", count);
+               ptr = RARRAY_PTR(cells);
+               for (i = 0; i < count; i++) {
+                       if (TYPE(ptr[i]) != T_ARRAY)
+                               rb_raise(rb_eTypeError, "the cell parameter array contains non-array object at index %d", i);
+                       len2 = RARRAY_LEN(ptr[i]);
+                       if (len2 < 4)
+                               rb_raise(rb_eMolbyError, "the cell parameter should contain 4 vectors");
+                       ptr2 = RARRAY_PTR(ptr[i]);
+                       for (j = 0; j < 4; j++)
+                               VectorFromValue(ptr2[j], &vp2[i * 4 + j]);
+               }
+       }
        ival = MolActionCreateAndPerform(mol, gMolActionInsertFrames, ig, mol->natoms * count, vp, (vp2 != NULL ? 4 * count : 0), vp2);
        IntGroupRelease(ig);
        free(vp);
@@ -6021,10 +6059,10 @@ s_Molecule_InsertFrames(int argc, VALUE *argv, VALUE self)
 static VALUE
 s_Molecule_CreateFrames(int argc, VALUE *argv, VALUE self)
 {
-       VALUE vals[2];
-       rb_scan_args(argc, argv, "01", &vals[1]);
+       VALUE vals[3];
+       rb_scan_args(argc, argv, "02", &vals[1], &vals[2]);
        vals[0] = Qnil;
-       return s_Molecule_InsertFrames(2, vals, self);
+       return s_Molecule_InsertFrames(3, vals, self);
 }
 
 /*