Include periodicity flags in the 'define unit cell' dialog

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@233 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/MolLib/MD/MDForce.c b/MolLib/MD/MDForce.c
index 795353e..96e9754 100644 (file)
--- a/MolLib/MD/MDForce.c
+++ b/MolLib/MD/MDForce.c
@@ -647,7 +647,7 @@ s_make_verlet_list(MDArena *arena)
                        VecSub(rij, apj->r, api->r);
 
                        /*  Calculate the cell offset for the nearest neighbor  */
-                       if (apj->periodic_exclude == 0 && cell != NULL) {
+                       if (ndx + ndy + ndz != 0 && apj->periodic_exclude == 0 && cell != NULL) {
                                count = s_enum_neighbors(arena, rij, limit);
                        } else {
                                static Int sZeros[3] = {0, 0, 0};

diff --git a/MolLib/Ruby_bind/ruby_md.c b/MolLib/Ruby_bind/ruby_md.c
index 82cc646..b28e72b 100644 (file)
--- a/MolLib/Ruby_bind/ruby_md.c
+++ b/MolLib/Ruby_bind/ruby_md.c
@@ -322,8 +322,8 @@ s_EnergyOutputFreqSym, s_CoordFrameSym, s_TimestepSym, s_CutoffSym,
 s_ElectroCutoffSym, s_PairlistDistanceSym, s_TemperatureSym, s_TransientTempSym, 
 s_AverageTempSym, s_AndersenFreqSym, s_AndersenCouplingSym, s_RandomSeedSym, 
 s_DielectricSym, s_GradientConvergenceSym, s_CoordinateConvergenceSym, s_UseXplorShiftSym, 
-s_Scale14VdwSym, s_Scale14ElectSym, s_RelocateCenterSym, s_SurfaceProbeRadiusSym, 
-s_SurfaceTensionSym, s_SurfacePotentialFreqSym, s_UseGraphiteSym,
+s_Scale14VdwSym, s_Scale14ElectSym, s_RelocateCenterSym, 
+s_SurfaceProbeRadiusSym, s_SurfaceTensionSym, s_SurfacePotentialFreqSym, s_UseGraphiteSym,
 s_AlchemicalLambdaSym, s_AlchemicalDeltaLambdaSym, s_AlchemicalEnergySym;
 
 struct s_MDArenaAttrDef {

diff --git a/MolLib/cmdtool_stubs.c b/MolLib/cmdtool_stubs.c
index 4299fab..7b490bb 100644 (file)
--- a/MolLib/cmdtool_stubs.c
+++ b/MolLib/cmdtool_stubs.c
@@ -262,6 +262,28 @@ MolActionCallback_registerUndo(Molecule *mol, MolAction *action)
 {
 }
 
+void
+MainView_setBackgroundColor(MainView *mview, float red, float green, float blue)
+{
+}
+
+void
+MainView_getBackgroundColor(const MainView *mview, float *rgb)
+{
+}
+
+int
+MainView_insertGraphic(MainView *mview, int index, const MainViewGraphic *graphic)
+{
+       return 0;
+}
+
+int
+MainView_removeGraphic(MainView *mview, int index)
+{
+       return 0;
+}
+
 int
 main(int argc, const char **argv)
 {

diff --git a/Scripts/md.rb b/Scripts/md.rb
index 61baeec..68839c0 100755 (executable)
--- a/Scripts/md.rb
+++ b/Scripts/md.rb
@@ -185,7 +185,8 @@ class Molecule
                bx = Vector3D[h["b0"], h["b1"], h["b2"]]
                cx = Vector3D[h["c0"], h["c1"], h["c2"]]
                ox = Vector3D[h["o0"], h["o1"], h["o2"]]
-               @mol.set_box(ax, bx, cx, ox)
+               fx = [value("aflag").to_i, value("bflag").to_i, value("cflag").to_i]
+               @mol.set_box(ax, bx, cx, ox, fx)
                return @mol
          end
 #        def action(item1)
@@ -197,25 +198,30 @@ class Molecule
 #              super
 #        end
          box = @mol.box
-         layout(4,
+         layout(5,
            item(:text, :title=>"Unit cell:"),
                -1, -1, -1,
+               item(:text, :title=>"Enable"),
            item(:text, :title=>"origin"),
                item(:textfield, :width=>140, :tag=>"o0", :value=>(box ? box[3].x.to_s : "")),
                item(:textfield, :width=>140, :tag=>"o1", :value=>(box ? box[3].y.to_s : "")),
                item(:textfield, :width=>140, :tag=>"o2", :value=>(box ? box[3].z.to_s : "")),
+               -1,
            item(:text, :title=>"a-axis"),
                item(:textfield, :width=>140, :tag=>"a0", :value=>(box ? box[0].x.to_s : "")),
                item(:textfield, :width=>140, :tag=>"a1", :value=>(box ? box[0].y.to_s : "")),
                item(:textfield, :width=>140, :tag=>"a2", :value=>(box ? box[0].z.to_s : "")),
+               item(:checkbox, :title=>"", :tag=>"aflag", :value=>(box ? box[4][0] : 0)),
            item(:text, :title=>"b-axis"),
                item(:textfield, :width=>140, :tag=>"b0", :value=>(box ? box[1].x.to_s : "")),
                item(:textfield, :width=>140, :tag=>"b1", :value=>(box ? box[1].y.to_s : "")),
                item(:textfield, :width=>140, :tag=>"b2", :value=>(box ? box[1].z.to_s : "")),
+               item(:checkbox, :title=>"", :tag=>"bflag", :value=>(box ? box[4][1] : 0)),
            item(:text, :title=>"c-axis"),
                item(:textfield, :width=>140, :tag=>"c0", :value=>(box ? box[2].x.to_s : "")),
                item(:textfield, :width=>140, :tag=>"c1", :value=>(box ? box[2].y.to_s : "")),
                item(:textfield, :width=>140, :tag=>"c2", :value=>(box ? box[2].z.to_s : "")),
+               item(:checkbox, :title=>"", :tag=>"cflag", :value=>(box ? box[4][2] : 0)),
                item(:button, :title=>"Set", :action=>:set_box_value),
                item(:text, :title=>"(Ruby expressions are allowed as the values)"),
                -1, -1)