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Merge pull request #1418 from virtualcell/dan-ss-options-panel
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 Integrator filtering offers unsuitable options for SpringSaLaD applications
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@danv61
danv61 authored Jan 14, 2025
2 parents d9ca79b + e44c236 commit 49a20b3
Showing 1 changed file with 52 additions and 18 deletions.
70 changes: 52 additions & 18 deletions vcell-core/src/main/java/cbit/vcell/solver/SolverDescription.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,14 +13,7 @@

import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.*;

import org.apache.commons.io.IOUtils;

Expand Down Expand Up @@ -116,7 +109,12 @@ public enum SolverDescription {

Smoldyn(TimeStep.CONSTANT, ErrorTol.NO, TimeSpecCreated.UNIFORM, "Smoldyn","Smoldyn (Spatial Stochastic Simulator)","Smoldyn (Spatial Stochastic Simulator)",
SolverLongDesc.SMOLDYN, 1,SupportedTimeSpec.UNIFORM,
new SolverFeature[]{SolverFeature.Feature_Spatial, SolverFeature.Feature_Stochastic, SolverFeature.Feature_PeriodicBoundaryCondition, SolverFeature.Feature_DataProcessingInstructions},
new SolverFeature[]{
SolverFeature.Feature_Spatial,
SolverFeature.Feature_Stochastic,
SolverFeature.Feature_PeriodicBoundaryCondition,
SolverFeature.Feature_DataProcessingInstructions,
SolverFeature.Feature_Smoldyn},
SolverExecutable.Smoldyn, "KISAO:0000057", false),

Chombo(TimeStep.CONSTANT, ErrorTol.NO, TimeSpecCreated.UNIFORM, "EBChombo","EBChombo, Semi-Implicit (Fixed Time Step), Experimental","Chombo Standalone",
Expand Down Expand Up @@ -188,6 +186,7 @@ public enum SolverFeature {
Feature_Hybrid("Hybrid: both Deterministic and Stochastic"),
Feature_Moving("Moving Membrane"),
Feature_Springs("Spring connected Sites"),
Feature_Smoldyn("Requires Smoldyn"),
;

private final String name;
Expand All @@ -199,6 +198,18 @@ public final String getName() {
}
}

// useful for debugging, makes easy to know which is the current SolverFeatureSet we're dealing with
public class SolverFeatureSetRegistry {
private static final Map<Object, String> nameRegistry = new LinkedHashMap<>();

public static void registerSolverFeatureSet(Object obj, String name) {
nameRegistry.put(obj, name);
}
public static String getSolverFeatureSetName(Object obj) {
return nameRegistry.get(obj);
}
}

/*
* Spatial solvers
*/
Expand All @@ -207,42 +218,56 @@ public final String getName() {
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements desc) {
return desc.isSpatialHybrid() && !desc.isMovingMembrane(); }},
FiniteVolumeStandalone,50);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(SpatialHybridFeatureSet, "SpatialHybridFeatureSet"); }

public static final SolverFeatureSet SpatialStochasticFeatureSet = new SolverFeatureSet (
new SolverFeature[] { SolverFeature.Feature_Spatial, SolverFeature.Feature_Stochastic },
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements desc) {
return desc.isSpatialStoch() && !desc.isSpatialHybrid(); }},
new SolverFeature[] { SolverFeature.Feature_Spatial, SolverFeature.Feature_Stochastic, SolverFeature.Feature_Smoldyn },
new SupportedProblemRequirements() {
public boolean supports(ProblemRequirements desc) {
boolean ret = desc.isSpatialStoch() && !desc.isSpatialHybrid() && !desc.isLangevin();
return ret;
}
},
Smoldyn,40);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(SpatialStochasticFeatureSet, "SpatialStochasticFeatureSet"); }

public static final SolverFeatureSet PdeFastSystemFeatureSet = new SolverFeatureSet (
new SolverFeature[] { SolverFeature.Feature_Spatial, SolverFeature.Feature_Deterministic, SolverFeature.Feature_FastSystem },
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements desc) {
return desc.isSpatial() && !desc.isSpatialHybrid() && desc.hasFastSystems( ) && !desc.isSpatialStoch(); }},
FiniteVolumeStandalone,30);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(PdeFastSystemFeatureSet, "PdeFastSystemFeatureSet"); }

public static final SolverFeatureSet PdeFeatureSetWithDirichletAtMembrane = new SolverFeatureSet(
new SolverFeature[] { SolverFeature.Feature_DirichletAtMembraneBoundary },
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements s) {
return s.isSpatial() && !s.isSpatialHybrid( ) && s.hasDirichletAtMembrane() && !s.hasFastSystems() && !s.isSpatialStoch(); }},
Chombo,20);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(PdeFeatureSetWithDirichletAtMembrane, "PdeFeatureSetWithDirichletAtMembrane"); }

public static final SolverFeatureSet PdeFeatureSetWithoutDirichletAtMembrane = new SolverFeatureSet(
new SolverFeature[] { SolverFeature.Feature_Spatial, SolverFeature.Feature_Deterministic },
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements s) {
return s.isSpatial() && !s.isSpatialHybrid() && !s.isMovingMembrane() && !s.hasDirichletAtMembrane() && !s.hasFastSystems() && !s.isSpatialStoch(); }},
boolean ret = s.isSpatial() && !s.isSpatialHybrid() && !s.isMovingMembrane() && !s.hasDirichletAtMembrane() && !s.hasFastSystems() && !s.isSpatialStoch() && !s.isLangevin();
return ret;
}},
SundialsPDE,10);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(PdeFeatureSetWithoutDirichletAtMembrane, "PdeFeatureSetWithoutDirichletAtMembrane"); }

// public static final SolverFeatureSet ComsolFeatureSet = new SolverFeatureSet(
// new SolverFeature[] { SolverFeature.Feature_Spatial,SolverFeature.Feature_Deterministic },
// new SupportedProblemRequirements() { public boolean supports(ProblemRequirements s) {
// return s.isSpatial() && !s.isSpatialHybrid() && !s.hasFastSystems() && !s.isSpatialStoch(); }},
// Comsol,30);
//
// static { VariableNameRegistry.registerVariable(ComsolFeatureSet, "ComsolFeatureSet"); }

public static final SolverFeatureSet MovingBoundaryFeatureSet = new SolverFeatureSet(
new SolverFeature[] { SolverFeature.Feature_Moving,SolverFeature.Feature_Spatial,SolverFeature.Feature_Deterministic },
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements s) {
return s.isSpatial() && !s.isSpatialHybrid() && s.isMovingMembrane() && !s.hasFastSystems() && !s.isSpatialStoch(); }},
boolean ret = s.isSpatial() && !s.isSpatialHybrid() && s.isMovingMembrane() && !s.hasFastSystems() && !s.isSpatialStoch();
return ret; }},
MovingBoundary,30);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(MovingBoundaryFeatureSet, "MovingBoundaryFeatureSet"); }

/*
* rule-based solvers
Expand All @@ -251,11 +276,14 @@ public final String getName() {
new SolverFeature[] { SolverFeature.Feature_NonSpatial, SolverFeature.Feature_Rulebased },
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements desc) { return desc.isRuleBased(); }},
NFSim,100);

static { SolverFeatureSetRegistry.registerSolverFeatureSet(RulebasedFeatureSet, "RulebasedFeatureSet"); }

public static final SolverFeatureSet LangevinFeatureSet = new SolverFeatureSet (
new SolverFeature[] { SolverFeature.Feature_Spatial, SolverFeature.Feature_Rulebased, SolverFeature.Feature_Springs },
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements desc) { return (desc.isLangevin()); }},
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements desc) {
return (desc.isLangevin()); }},
Langevin,200);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(LangevinFeatureSet, "LangevinFeatureSet"); }

/*
* Non-spatial solvers
Expand All @@ -264,18 +292,21 @@ public final String getName() {
new SolverFeature[] { SolverFeature.Feature_NonSpatial, SolverFeature.Feature_Stochastic},
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements desc) { return desc.isNonSpatialStoch() && !desc.isRuleBased(); }},
StochGibson,100);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(NonSpatialStochasticFeatureSet, "NonSpatialStochasticFeatureSet"); }

public static final SolverFeatureSet OdeFeatureSet = new SolverFeatureSet(
new SolverFeature[] { SolverFeature.Feature_NonSpatial, SolverFeature.Feature_Deterministic},
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements desc) {
return !desc.isSpatial() && !desc.hasFastSystems() && !desc.isNonSpatialStoch() && !desc.isRuleBased(); }},
CombinedSundials,10);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(OdeFeatureSet, "OdeFeatureSet"); }

public static final SolverFeatureSet OdeFastSystemFeatureSet = new SolverFeatureSet(
new SolverFeature[] { SolverFeature.Feature_NonSpatial, SolverFeature.Feature_Deterministic, SolverFeature.Feature_FastSystem},
new SupportedProblemRequirements() { public boolean supports(ProblemRequirements desc) {
return !desc.isSpatial() && desc.hasFastSystems() && !desc.isNonSpatialStoch() && !desc.isRuleBased(); }},
CombinedSundials,10);
static { SolverFeatureSetRegistry.registerSolverFeatureSet(OdeFastSystemFeatureSet, "OdeFastSystemFeatureSet"); }

//this one is not like the others
public static final Collection<SolverFeature> DiscontinutiesFeatures = Arrays.asList(new SolverFeature[]{
Expand Down Expand Up @@ -658,8 +689,11 @@ public static Collection<SolverDescription> getSupportingSolverDescriptions(Prob
ProblemRequirements.Checker.validate(mathDescription);
Collection<SolverDescription> solvers = new HashSet<SolverDescription>( );
for (SolverFeatureSet sfs : SolverFeatureSet.getSets()) {
System.out.println(SolverFeatureSetRegistry.getSolverFeatureSetName(sfs));
if (sfs.supports(mathDescription)) {
solvers.addAll(getSolverDescriptions(sfs.getSolverFeatures()));
List<SolverFeature> solverFeatures = sfs.getSolverFeatures();
Collection<SolverDescription> solverDescriptions = getSolverDescriptions(solverFeatures);
solvers.addAll(solverDescriptions);
}
}
if (!solvers.isEmpty( )) {
Expand Down

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