// Set visibility of grid data
bool Commands::function_GridVisible(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
if (c->hasArg(0)) obj.g->setVisible(c->argb(0));
rv.set(obj.g->isVisible());
return true;
}
// Add next gridpoint in sequence
bool Commands::function_AddNextGridPoint(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
obj.g->setNextData(c->argd(0));
rv.reset();
return true;
}
// Set whether 2D grid uses data value as height component
bool Commands::function_GridUseZ(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
if (c->hasArg(0)) obj.g->setUseDataForZ(c->argb(0));
rv.set(obj.g->useDataForZ());
return true;
}
// Set view percentage for secondary surface
bool Commands::function_GridViewPercentageSecondary(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
if (c->hasArg(0)) obj.g->setSecondaryCutoffAsViewPercentage(c->argd(0), c->hasArg(1) ? c->argb(1) : false);
rv.set((obj.g->partialSecondarySum() / obj.g->totalAbsoluteSum())*100.0);
return true;
}
// Set whether grid is periodic
bool Commands::function_GridPeriodic(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
obj.g->setPeriodic(c->argb(0));
rv.reset();
return true;
}
// Set secondary grid cutoff
bool Commands::function_GridCutoffSecondary(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
obj.g->setLowerSecondaryCutoff(c->argd(0));
if (c->hasArg(1)) obj.g->setUpperSecondaryCutoff(c->argd(1));
rv.reset();
return true;
}
// Set negative colour for grid
bool Commands::function_GridColourSecondary(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
if (c->hasArg(3)) obj.g->setSecondaryColour(c->argd(0), c->argd(1), c->argd(2), c->argd(3));
else obj.g->setSecondaryColour(c->argd(0), c->argd(1), c->argd(2));
rv.reset();
return true;
}
// Set transparency of primary and secondary grid surfaces
bool Commands::function_GridAlpha(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
obj.g->setPrimaryAlpha(c->argGLf(0));
obj.g->setSecondaryAlpha(c->argGLf(0));
rv.reset();
return true;
}
// Clears charge in current model ('clearcharges')
bool Commands::function_ClearCharges(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
obj.rs()->beginUndoState("Remove charges");
obj.rs()->clearCharges();
obj.rs()->endUndoState();
return true;
}
// Assign charge to a pattern atom, propagated over the model ('chargepatom <id> <q>')
bool Commands::function_ChargePAtom(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
obj.rs()->beginUndoState("Charge single pattern atom");
obj.rs()->chargePatternAtom(obj.p,c->argi(0),c->argd(1));
obj.rs()->endUndoState();
return true;
}
// Assign charges from forcefield atom types ('chargeff')
bool Commands::function_ChargeFF(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
obj.rs()->beginUndoState("Assign forcefield charges");
bool result = obj.rs()->assignForcefieldCharges();
obj.rs()->endUndoState();
return (result);
}
// Add grid point data at specified indices
bool Commands::function_AddGridPoint(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
Vec3<int> veci = c->arg3i(0);
obj.g->setData(veci.x-1, veci.y-1, veci.z-1, c->argd(3));
rv.reset();
return true;
}
// Create new grid in the current model
bool Commands::function_NewGrid(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
obj.g = aten_.currentModel()->addGrid();
obj.g->setName(c->argc(0).trimmed());
rv.set(VTypes::GridData, obj.g);
return true;
}
// Initialise grid, setting extent of grid (number of points in each direction)
bool Commands::function_InitialiseGrid(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
Grid::GridType gt = Grid::gridType(c->argc(0), true);
if (gt == Grid::nGridTypes) return false;
rv.set(obj.g->initialise(gt, c->arg3i(1)));
return true;
}
// Set drawing style of secondary surface
bool Commands::function_GridStyleSecondary(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
Grid::SurfaceStyle ss = Grid::surfaceStyle(c->argc(0));
if (ss == Grid::nSurfaceStyles) return false;
obj.g->setSecondaryStyle(ss);
rv.reset();
return true;
}
ATEN_USING_NAMESPACE
// Add free grid point data at specified coordinates
bool Commands::function_AddFreePoint(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
obj.g->addFreePoint(c->argd(0), c->argd(1), c->argd(2), c->argd(3));
rv.reset();
return true;
}
// Copy atomic charges from model to model's current trajectory frame
bool Commands::function_ChargeFromModel(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
if (obj.rs() == obj.m)
{
Messenger::print("Error - 'chargefrommodel' requires an active trajectory frame in the current model.");
return false;
}
else obj.rs()->copyAtomData(obj.m, Atom::ChargeData);
return true;
}
// Set grid axes (nine doubles)
bool Commands::function_GridAxes(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
Matrix mat;
mat.setColumn(0, c->arg3d(0), 0.0);
mat.setColumn(1, c->arg3d(3), 0.0);
mat.setColumn(2, c->arg3d(6), 0.0);
obj.g->setAxes(mat);
rv.reset();
return true;
}
// Load grid ('loadgrid <filename>')
bool Commands::function_LoadGrid(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
Grid* g = NULL;
if (aten_.importGrid(obj.rs(), c->argc(0))) g = obj.g;
else return false;
// Set return value
rv.set(VTypes::GridData, g);
return true;
}
// Set colour scale for grid
bool Commands::function_GridColourscale(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
int cs = c->argi(0);
if ((cs < 0) || (cs > 10))
{
Messenger::print("ColourScale %i is out of range (1-10, or 0 to use object's internal colour).",cs);
return false;
}
obj.g->setColourScale(cs-1);
rv.reset();
return true;
}
// Set loop order to use in 'gridnextpoint'
bool Commands::function_GridLoopOrder(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
if (c->argc(0).length() != 3)
{
Messenger::print("A string of three characters must be passed to 'gridLoopOrder' (got '%s').", qPrintable(c->argc(0)));
return false;
}
obj.g->setLoopOrder(c->argc(0));
rv.reset();
return true;
}
// Return nth grid of model
bool Commands::function_GetGrid(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
Grid* g = NULL;
switch (c->argType(0))
{
case (VTypes::IntegerData):
g = obj.rs()->grid(c->argi(0)-1);
break;
case (VTypes::GridData):
g = (Grid*) c->argp(0, VTypes::GridData);
break;
default:
Messenger::print("Can't convert a variable of type '%s' to a Grid.", VTypes::dataType(c->argType(0)));
break;
}
if (g == NULL) return false;
rv.set(VTypes::GridData, g);
return true;
}
ATEN_USING_NAMESPACE
// Assign charge to selected atoms in model ('charge <q>'), or get charge of current selection
bool Commands::function_Charge(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
double q = 0.0;
if (c->hasArg(0))
{
obj.rs()->beginUndoState("Charge selected atoms");
for (RefListItem<Atom,int>* ri = obj.rs()->selection(); ri != NULL; ri = ri->next) obj.rs()->atomSetCharge(ri->item, c->argd(0));
obj.rs()->endUndoState();
}
else
{
q = 0.0;
for (RefListItem<Atom,int>* ri = obj.rs()->selection(); ri != NULL; ri = ri->next) q += ri->item->charge();
}
rv.set(q);
return true;
}
