Refactor EnergyBase for increased readability (#296)

* Renaming refactor for energybase and external potential * variable renaming and schema update
mlund · Jun 28, 2020 · 4fb92dd · 4fb92dd
1 parent 74fe32a
commit 4fb92dd
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Showing 6 changed files with 197 additions and 181 deletions.
diff --git a/docs/schema.yml b/docs/schema.yml
@@ -530,7 +530,24 @@ properties:
                                           - required: [rhoinv]
                                           - required: [phi0]
                                       additionalProperties: false
-
+                akesson:
+                    description: "Electric potential correction from outside cuboidal slit"
+                    type: object
+                    properties:
+                        dz: {type: number, default: 0.2, description: "resolution along z (Å)"}
+                        epsr: {type: number, description: "Relative dielectric constant"}
+                        file: {type: string, description: "Input/output file for charge density profile"}
+                        nphi: {type: integer, default: 10, description: "Multiple of `nstep` in between updating charge density profile"}
+                        fixed: {type: boolean, default: false, description: "If true, do not update loaded charge density"}
+                        nstep: {type: integer, description: "Number of energy evalutations between updating charge density"}
+                        molecules:
+                            type: array
+                            items: {type: string}
+                            minItems: 1
+                            description: "Array of molecules to operate on"
+                    required: [epsr, molecules, nstep]
+                    additionalProperties: false
+
                 isobaric:
                     description: "External pressure"
                     type: object

diff --git a/src/energy.cpp b/src/energy.cpp
@@ -344,7 +344,7 @@ double PolicyIonIonEigen::reciprocalEnergy(const EwaldData &d) {
 Ewald::Ewald(const json &j, Space &spc) : data(j), spc(spc) {
     name = "ewald";
     policy = EwaldPolicyBase::makePolicy(data.policy);
-    cite = policy->cite;
+    citation_information = policy->cite;
     init();
 }
 
@@ -356,8 +356,8 @@ void Ewald::init() {
 double Ewald::energy(Change &change) {
     double u = 0;
     if (change) {
-        // If the state is NEW (trial state), then update all k-vectors
-        if (key == NEW) {
+        // If the state is NEW_MONTE_CARLO_STATE (trial state), then update all k-vectors
+        if (key == NEW_MONTE_CARLO_STATE) {
             if (change.all or change.dV) { // everything changes
                 policy->updateBox(data, spc.geo.getLength());
                 policy->updateComplex(data, spc.groups); // update all (expensive!)
@@ -381,10 +381,10 @@ double Ewald::energy(Change &change) {
 void Ewald::sync(Energybase *energybase_pointer, Change &change) {
     auto other = dynamic_cast<decltype(this)>(energybase_pointer);
     assert(other);
-    if (other->key == OLD) {
-      old_groups =
-          &(other->spc
-                .groups); // give NEW access to OLD space for optimized updates
+    if (other->key == OLD_MONTE_CARLO_STATE) {
+        old_groups =
+            &(other->spc
+                  .groups); // give NEW_MONTE_CARLO_STATE access to OLD_MONTE_CARLO_STATE space for optimized updates
     }
 
     // hard-coded sync; should be expanded when dipolar ewald is supported
@@ -449,7 +449,7 @@ double ContainerOverlap::energy(Change &change) {
 
 Isobaric::Isobaric(const json &j, Space &spc) : spc(spc) {
     name = "isobaric";
-    cite = "Frenkel & Smith 2nd Ed (Eq. 5.4.13)";
+    citation_information = "Frenkel & Smith 2nd Ed (Eq. 5.4.13)";
     P = j.value("P/mM", 0.0) * 1.0_mM;
     if (P < 1e-10) {
         P = j.value("P/Pa", 0.0) * 1.0_Pa;
@@ -762,7 +762,7 @@ SASAEnergy::SASAEnergy(Space &spc, double cosolute_concentration, double probe_r
     : spc(spc), cosolute_concentration(cosolute_concentration)
 {
     name = "sasa"; // todo predecessor constructor
-    cite = "doi:10.12688/f1000research.7931.1"; // todo predecessor constructor
+    citation_information = "doi:10.12688/f1000research.7931.1"; // todo predecessor constructor
     parameters = freesasa_default_parameters;
     parameters.probe_radius = probe_radius;
     init();

diff --git a/src/energy.h b/src/energy.h
@@ -1023,7 +1023,7 @@ template <typename Tpairpot> class NonbondedCached : public Nonbonded<PairingPol
         if (j < i) {
             std::swap(i, j);
         }
-        if (base::key == Energybase::NEW) { // if this is from the trial system,
+        if (base::key == Energybase::NEW_MONTE_CARLO_STATE) { // if this is from the trial system,
             cache(i, j) = base::pairing.group2group(g1, g2); // update the cache
         }
         return cache(i, j); // return (cached) value