Substantial rework of occ cg outputs, renaming lots of fields in JSON…

… etc.
peterspackman · Jan 9, 2025 · 1cd58a0 · 1cd58a0
1 parent 686f333
commit 1cd58a0
Show file tree

Hide file tree

Showing 15 changed files with 282 additions and 275 deletions.
diff --git a/3rdparty/CMakeLists.txt b/3rdparty/CMakeLists.txt
@@ -1,35 +1,35 @@
 CPMAddPackage(
     NAME fmt
     GITHUB_REPOSITORY "fmtlib/fmt"
-    VERSION "11.0.1"
-    GIT_TAG "11.0.1"
+    VERSION "11.0.2"
+    GIT_TAG "11.0.2"
 )
 
 CPMAddPackage(
     NAME spdlog
     GITHUB_REPOSITORY "gabime/spdlog"
     OPTIONS "SPDLOG_FMT_EXTERNAL ON"
-    VERSION "1.14.1"
+    VERSION "1.15.0"
 )
 
 CPMAddPackage(
     NAME unordered_dense
     GITHUB_REPOSITORY "martinus/unordered_dense"
-    VERSION "4.1.2"
+    VERSION "4.5.0"
 )
 
 CPMAddPackage(
     NAME scnlib
     GITHUB_REPOSITORY "eliaskosunen/scnlib"
-    VERSION "2.0.2"
+    VERSION "4.0.1"
     OPTIONS "SIMDUTF_TESTS OFF" "ENABLE_FULL OFF"
 )
 
 
 CPMAddPackage(
     NAME CLI11
     GITHUB_REPOSITORY "CLIUtils/CLI11"
-    VERSION "2.4.1"
+    VERSION "2.4.2"
 )
 
 if("${USE_MLX}")

diff --git a/cmake/CPM.cmake b/cmake/CPM.cmake
@@ -2,8 +2,8 @@
 #
 # SPDX-FileCopyrightText: Copyright (c) 2019-2023 Lars Melchior and contributors
 
-set(CPM_DOWNLOAD_VERSION 0.40.2)
-set(CPM_HASH_SUM "c8cdc32c03816538ce22781ed72964dc864b2a34a310d3b7104812a5ca2d835d")
+set(CPM_DOWNLOAD_VERSION 0.40.5)
+set(CPM_HASH_SUM "c46b876ae3b9f994b4f05a4c15553e0485636862064f1fcc9d8b4f832086bc5d")
 
 if(CPM_SOURCE_CACHE)
   set(CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")

diff --git a/include/occ/cg/crystal_growth_energies.h b/include/occ/cg/crystal_growth_energies.h
diff --git a/include/occ/cg/interaction_mapper.h b/include/occ/cg/interaction_mapper.h
@@ -1,5 +1,5 @@
 #pragma once
-#include <occ/cg/crystal_growth_energies.h>
+#include <occ/cg/result_types.h>
 #include <occ/crystal/crystal.h>
 #include <occ/crystal/dimer_mapping_table.h>
 
@@ -20,26 +20,26 @@ class InteractionMapper {
 
   std::vector<double>
   map_interactions(const std::vector<double> &solution_terms,
-                   const std::vector<Energies> &interaction_energies_vec);
+                   const std::vector<DimerResults> &interaction_energies_vec);
 
 private:
   void map_molecule_interactions(
       size_t mol_idx, const Molecule &mol,
       const std::vector<double> &solution_terms,
-      const std::vector<Energies> &interaction_energies_vec,
+      const std::vector<DimerResults> &interaction_energies_vec,
       std::vector<double> &solution_terms_uc);
 
   void map_neighbor_interactions(
       size_t mol_idx,
       std::vector<CrystalDimers::SymmetryRelatedDimer> &unit_cell_neighbors,
       const std::vector<CrystalDimers::SymmetryRelatedDimer>
           &asymmetric_neighbors,
-      const Energies &interaction_energies);
+      const DimerResults &interaction_energies);
 
   void map_single_dimer(size_t mol_idx, size_t neighbor_idx, Dimer &dimer,
                         const std::vector<CrystalDimers::SymmetryRelatedDimer>
                             &asymmetric_neighbors,
-                        const Energies &interaction_energies);
+                        const DimerResults &interaction_energies);
 
   ankerl::unordered_dense::set<DimerIndex, DimerIndexHash>
   build_related_set(const std::vector<DimerIndex> &related) const;
@@ -57,7 +57,7 @@ class InteractionMapper {
   void update_dimer_properties(
       Dimer &dimer, size_t interaction_id,
       const std::vector<CrystalDimers::SymmetryRelatedDimer> &asym_dimers,
-      const Energies &energies) const;
+      const DimerResults &energies) const;
 
   void log_neighbor_info(size_t mol_idx, size_t uc_neighbors_size,
                          size_t asym_neighbors_size,

diff --git a/include/occ/cg/result_types.h b/include/occ/cg/result_types.h
@@ -1,16 +1,21 @@
 #pragma once
 #include <ankerl/unordered_dense.h>
+#include <occ/core/dimer.h>
+#include <occ/interaction/pairinteraction.h>
 #include <string>
 #include <vector>
 
 namespace occ::cg {
+
+using PairEnergies = std::vector<occ::interaction::CEEnergyComponents>;
 using CGEnergyComponents = ankerl::unordered_dense::map<std::string, double>;
+using CGEnergies = std::vector<CGEnergyComponents>;
 
 namespace components {
 
 constexpr const char *total = "Total";
 constexpr const char *crystal_total = "Crystal Total";
-constexpr const char *crystal_nn = "Crystal (reassigned)";
+constexpr const char *crystal_nn = "Crystal (redistributed)";
 constexpr const char *solvation_ab = "Solvation (A->B)";
 constexpr const char *solvation_ba = "Solvation (B->A)";
 constexpr const char *solvation_total = "Solvation Total";
@@ -22,9 +27,22 @@ constexpr const char *exchange = "Exchange";
 
 } // namespace components
 
+struct DimerSolventTerm {
+  double ab{0.0};
+  double ba{0.0};
+  double total{0.0};
+};
+
+struct EnergyTotal {
+  double crystal_energy{0.0};
+  double interaction_energy{0.0};
+  double solution_term{0.0};
+};
+
 struct DimerResult {
+  occ::core::Dimer dimer;
   bool is_nearest_neighbor{false};
-  size_t unique_idx{0};
+  int unique_idx{0};
 
   CGEnergyComponents energy_components{{components::total, 0.0},
                                        {components::crystal_total, 0.0},
@@ -38,6 +56,8 @@ struct DimerResult {
   bool has_energy_component(const std::string &key) const;
 };
 
+using DimerResults = std::vector<DimerResult>;
+
 struct MoleculeResult {
   CGEnergyComponents energy_components{{components::total, 0.0},
                                        {components::crystal_total, 0.0},
@@ -46,6 +66,8 @@ struct MoleculeResult {
   std::vector<DimerResult> dimer_results;
   bool has_inversion_symmetry{true};
 
+  cg::EnergyTotal total;
+
   double total_energy() const;
   void add_dimer_result(const DimerResult &dimer);
 

diff --git a/include/occ/core/dimer.h b/include/occ/core/dimer.h
@@ -27,6 +27,9 @@ class Dimer {
     BA = false /**< The B molecule data is first, then A */
   };
 
+  // Default (empty) constructor.
+  Dimer() = default;
+
   /**
    * Constructor from two Molecule objects
    *
@@ -200,7 +203,7 @@ class Dimer {
    * \param e a double representing the interaction energy.
    * \param key a string labelling the component of the interaction energy.
    */
-  void set_interaction_energy(double e, const std::string &key = "total");
+  void set_interaction_energy(double e, const std::string &key = "Total");
 
   /**
    * Get the stored interaction energy for this Dimer.
@@ -209,7 +212,7 @@ class Dimer {
    *
    * \returns a double representing the interaction energy (default = 0.0)
    */
-  double interaction_energy(const std::string &key = "total") const;
+  double interaction_energy(const std::string &key = "Total") const;
 
   inline void set_interaction_energies(
       const ankerl::unordered_dense::map<std::string, double> &e) {

diff --git a/include/occ/driver/crystal_growth.h b/include/occ/driver/crystal_growth.h
@@ -1,6 +1,6 @@
 #pragma once
-#include <occ/cg/crystal_growth_energies.h>
 #include <occ/cg/distance_partition.h>
+#include <occ/cg/result_types.h>
 #include <occ/cg/smd_solvation.h>
 #include <occ/cg/solvation_contribution.h>
 #include <occ/cg/solvent_surface.h>
@@ -15,8 +15,6 @@
 #include <occ/interaction/pairinteraction.h>
 #include <occ/io/wavefunction_json.h>
 #include <occ/qm/wavefunction.h>
-#include <string>
-#include <vector>
 
 namespace occ::driver {
 
@@ -109,8 +107,7 @@ class CrystalGrowthCalculator {
   virtual void init_monomer_energies() = 0;
   virtual void converge_lattice_energy() = 0;
 
-  virtual std::tuple<cg::EnergyTotal, std::vector<cg::CrystalGrowthDimer>>
-  process_neighbors_for_symmetry_unique_molecule(
+  virtual cg::MoleculeResult process_neighbors_for_symmetry_unique_molecule(
       int i, const std::string &molname) = 0;
 
   virtual cg::CrystalGrowthResult evaluate_molecular_surroundings() = 0;
@@ -127,8 +124,8 @@ class CrystalGrowthCalculator {
   cg::PairEnergies m_dimer_energies;
   crystal::CrystalDimers m_nearest_dimers;
   std::vector<SolventNeighborContributionList> m_solvation_breakdowns;
-  std::vector<cg::Energies> m_interaction_energies;
-  std::vector<cg::Energies> m_crystal_interaction_energies;
+  std::vector<cg::DimerResults> m_interaction_energies;
+  std::vector<cg::DimerResults> m_crystal_interaction_energies;
   std::vector<double> m_solution_terms;
 
 private:
@@ -146,8 +143,7 @@ class CEModelCrystalGrowthCalculator : public CrystalGrowthCalculator {
 
   cg::CrystalGrowthResult evaluate_molecular_surroundings() override;
 
-  std::tuple<cg::EnergyTotal, std::vector<cg::CrystalGrowthDimer>>
-  process_neighbors_for_symmetry_unique_molecule(
+  cg::MoleculeResult process_neighbors_for_symmetry_unique_molecule(
       int i, const std::string &molname) override;
 };
 
@@ -162,8 +158,7 @@ class XTBCrystalGrowthCalculator : public CrystalGrowthCalculator {
 
   cg::CrystalGrowthResult evaluate_molecular_surroundings() override;
 
-  std::tuple<cg::EnergyTotal, std::vector<cg::CrystalGrowthDimer>>
-  process_neighbors_for_symmetry_unique_molecule(
+  cg::MoleculeResult process_neighbors_for_symmetry_unique_molecule(
       int i, const std::string &molname) override;
 
   std::vector<double> m_gas_phase_energies;

diff --git a/include/occ/io/crystalgrower.h b/include/occ/io/crystalgrower.h
@@ -1,35 +1,42 @@
 #pragma once
+#include <ankerl/unordered_dense.h>
 #include <fstream>
 #include <occ/crystal/crystal.h>
-#include <vector>
 
 namespace occ::io::crystalgrower {
 
 class StructureWriter {
-  public:
-    StructureWriter(const std::string &filename);
-    StructureWriter(std::ostream &);
-
-    void write(const occ::crystal::Crystal &,
-               const occ::crystal::CrystalDimers &);
-    void write_net(const occ::crystal::Crystal &,
-                   const occ::crystal::CrystalDimers &);
-
-  private:
-    std::ofstream m_owned_destination;
-    std::ostream &m_dest;
+public:
+  StructureWriter(const std::string &filename);
+  StructureWriter(std::ostream &);
+
+  void write(const occ::crystal::Crystal &,
+             const occ::crystal::CrystalDimers &);
+  void write_net(const occ::crystal::Crystal &,
+                 const occ::crystal::CrystalDimers &);
+
+private:
+  std::ofstream m_owned_destination;
+  std::ostream &m_dest;
 };
 
 class NetWriter {
-  public:
-    NetWriter(const std::string &filename);
-    NetWriter(std::ostream &);
+public:
+  using InteractionLabels =
+      ankerl::unordered_dense::map<std::string, std::string>;
+  NetWriter(const std::string &filename);
+  NetWriter(std::ostream &);
+
+  void write(const occ::crystal::Crystal &,
+             const occ::crystal::CrystalDimers &);
 
-    void write(const occ::crystal::Crystal &,
-               const occ::crystal::CrystalDimers &);
+  inline const InteractionLabels &interaction_labels() const {
+    return m_interaction_labels;
+  };
 
-  private:
-    std::ofstream m_owned_destination;
-    std::ostream &m_dest;
+private:
+  std::ofstream m_owned_destination;
+  std::ostream &m_dest;
+  InteractionLabels m_interaction_labels;
 };
 } // namespace occ::io::crystalgrower
diff --git a/include/occ/main/occ_cg.h b/include/occ/main/occ_cg.h
@@ -1,6 +1,6 @@
 #pragma once
 #include <CLI/App.hpp>
-#include <occ/cg/crystal_growth_energies.h>
+#include <occ/cg/result_types.h>
 #include <occ/core/dimer.h>
 #include <occ/interaction/pair_energy.h>