extend Subdomain with new functionality

examples/Argon/Argon.cpp

@@ -1,24 +1,23 @@
 // Copyright 2024 Sebastian Eibl
-// 
+//
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
 // You may obtain a copy of the License at
-// 
+//
 //     https://www.apache.org/licenses/LICENSE-2.0
-// 
+//
 // Unless required by applicable law or agreed to in writing, software
 // distributed under the License is distributed on an "AS IS" BASIS,
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-#include <format>
-
 #include <CLI/App.hpp>
 #include <CLI/Config.hpp>
 #include <CLI/Formatter.hpp>
 #include <Kokkos_Core.hpp>
 #include <algorithm>
+#include <format>
 #include <fstream>
 #include <iomanip>
 #include <iostream>
@@ -72,7 +71,7 @@ struct Config
 
     idx_t estimatedMaxNeighbors = 60;
 
-    const std::string resName = "Argon"; 
+    const std::string resName = "Argon";
     const std::vector<std::string> typeNames = {"Ar"};
 };
 
@@ -118,12 +117,19 @@ void LJ(Config& config)
 {
     auto subdomain =
         data::Subdomain({0_r, 0_r, 0_r}, {config.Lx, config.Lx, config.Lx}, config.neighborCutoff);
-    const auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
+    const auto volume = subdomain.getVolume();
     auto atoms = fillDomainWithAtomsSC(subdomain, config.numAtoms, 1_r);
     auto rho = real_c(atoms.numLocalAtoms) / volume;
     std::cout << "rho: " << rho << std::endl;
 
-    io::dumpGRO("atoms_initial.gro", atoms, subdomain, 0_r, "Argon", config.resName, config.typeNames, false);
+    io::dumpGRO("atoms_initial.gro",
+                atoms,
+                subdomain,
+                0_r,
+                "Argon",
+                config.resName,
+                config.typeNames,
+                false);
 
     communication::GhostLayer ghostLayer;
     action::LennardJones LJ(config.rc, config.sigma, config.epsilon, 0.7_r * config.sigma);

examples/Argon/MultiResArgon.cpp

@@ -1,24 +1,23 @@
 // Copyright 2024 Sebastian Eibl
-// 
+//
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
 // You may obtain a copy of the License at
-// 
+//
 //     https://www.apache.org/licenses/LICENSE-2.0
-// 
+//
 // Unless required by applicable law or agreed to in writing, software
 // distributed under the License is distributed on an "AS IS" BASIS,
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-#include <format>
-
 #include <CLI/App.hpp>
 #include <CLI/Config.hpp>
 #include <CLI/Formatter.hpp>
 #include <Kokkos_Core.hpp>
 #include <algorithm>
+#include <format>
 #include <fstream>
 #include <iomanip>
 #include <iostream>
@@ -76,9 +75,8 @@ struct Config
 
     idx_t estimatedMaxNeighbors = 60;
 
-    const std::string resName = "Argon"; 
+    const std::string resName = "Argon";
     const std::vector<std::string> typeNames = {"Ar"};
-
 };
 
 data::Atoms fillDomainWithAtomsSC(const data::Subdomain& subdomain,
@@ -125,13 +123,20 @@ void LJ(Config& config)
 {
     auto subdomain =
         data::Subdomain({0_r, 0_r, 0_r}, {config.Lx, config.Lx, config.Lx}, config.neighborCutoff);
-    const auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
+    const auto volume = subdomain.getVolume();
     auto atoms = fillDomainWithAtomsSC(subdomain, config.numAtoms, 1_r);
     auto molecules = data::createMoleculeForEachAtom(atoms);
     auto rho = real_c(atoms.numLocalAtoms) / volume;
     std::cout << "rho: " << rho << std::endl;
 
-    io::dumpGRO("atoms_initial.gro", atoms, subdomain, 0_r, "Argon", config.resName, config.typeNames, false);
+    io::dumpGRO("atoms_initial.gro",
+                atoms,
+                subdomain,
+                0_r,
+                "Argon",
+                config.resName,
+                config.typeNames,
+                false);
 
     communication::MultiResGhostLayer ghostLayer;
     weighting_function::Slab weightingFunction({-100_r, -100_r, -100_r}, 1_r, 1_r, 1);
@@ -230,7 +235,7 @@ void LJ(Config& config)
                         subdomain,
                         step * config.dt,
                         "Argon",
-                        config.resName, 
+                        config.resName,
                         config.typeNames,
                         false);
 

examples/BinaryLennardJones/NPT.cpp

@@ -1,11 +1,11 @@
 // Copyright 2024 Sebastian Eibl
-// 
+//
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
 // You may obtain a copy of the License at
-// 
+//
 //     https://www.apache.org/licenses/LICENSE-2.0
-// 
+//
 // Unless required by applicable law or agreed to in writing, software
 // distributed under the License is distributed on an "AS IS" BASIS,
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -14,9 +14,8 @@
 
 #include "NPT.hpp"
 
-#include <format>
-
 #include <algorithm>
+#include <format>
 
 #include "action/BerendsenBarostat.hpp"
 #include "action/BerendsenThermostat.hpp"
@@ -38,7 +37,7 @@ void npt(YAML::Node& config, data::Atoms& atoms, data::Subdomain& subdomain)
     auto rcVec = config["LJ"]["cutoff"].as<std::vector<real_t>>();
     const real_t rc = std::ranges::max(rcVec);
     const real_t neighborCutoff = rc + skin;
-    auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
+    auto volume = subdomain.getVolume();
 
     communication::GhostLayer ghostLayer;
     auto LJ = action::LennardJones(config["LJ"]["capping"].as<std::vector<real_t>>(),
@@ -79,7 +78,7 @@ void npt(YAML::Node& config, data::Atoms& atoms, data::Subdomain& subdomain)
                                              false,
                                              true,
                                              false);
-            volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
+            volume = subdomain.getVolume();
             maxAtomDisplacement = std::numeric_limits<real_t>::max();
         }
 

examples/BinaryLennardJones/NVT.cpp

@@ -1,11 +1,11 @@
 // Copyright 2024 Sebastian Eibl
-// 
+//
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
 // You may obtain a copy of the License at
-// 
+//
 //     https://www.apache.org/licenses/LICENSE-2.0
-// 
+//
 // Unless required by applicable law or agreed to in writing, software
 // distributed under the License is distributed on an "AS IS" BASIS,
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -14,9 +14,8 @@
 
 #include "NVT.hpp"
 
-#include <format>
-
 #include <algorithm>
+#include <format>
 
 #include "action/BerendsenThermostat.hpp"
 #include "action/LennardJones.hpp"
@@ -37,7 +36,7 @@ void nvt(YAML::Node& config, data::Atoms& atoms, const data::Subdomain& subdomai
     auto rcVec = config["LJ"]["cutoff"].as<std::vector<real_t>>();
     const real_t rc = std::ranges::max(rcVec);
     const real_t neighborCutoff = rc + skin;
-    auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
+    auto volume = subdomain.getVolume();
 
     communication::GhostLayer ghostLayer;
     auto LJ = action::LennardJones(config["LJ"]["capping"].as<std::vector<real_t>>(),

examples/BinaryLennardJones/SPARTIAN.cpp

@@ -14,9 +14,8 @@
 
 #include "SPARTIAN.hpp"
 
-#include <format>
-
 #include <algorithm>
+#include <format>
 #include <fstream>
 
 #include "action/ContributeMoleculeForceToAtoms.hpp"
@@ -47,7 +46,7 @@ void spartian(YAML::Node& config,
     auto rcVec = config["LJ"]["cutoff"].as<std::vector<real_t>>();
     const real_t rc = std::ranges::max(rcVec);
     const real_t neighborCutoff = rc + skin;
-    auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
+    auto volume = subdomain.getVolume();
 
     communication::MultiResGhostLayer ghostLayer;
     auto LJ = action::LJ_IdealGas(config["LJ"]["capping"].as<std::vector<real_t>>(),

examples/DensityFluctuations/DensityFluctuations.cpp

@@ -1,23 +1,22 @@
 // Copyright 2024 Sebastian Eibl
-// 
+//
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
 // You may obtain a copy of the License at
-// 
+//
 //     https://www.apache.org/licenses/LICENSE-2.0
-// 
+//
 // Unless required by applicable law or agreed to in writing, software
 // distributed under the License is distributed on an "AS IS" BASIS,
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-#include <format>
-
 #include <CLI/App.hpp>
 #include <CLI/Config.hpp>
 #include <CLI/Formatter.hpp>
 #include <Kokkos_Core.hpp>
+#include <format>
 #include <fstream>
 #include <iomanip>
 #include <iostream>
@@ -86,7 +85,7 @@ struct Config
     // thermodynamic force parameters
     real_t thermodynamicForceModulation = 2.0_r;
 
-    const std::string resName = "Argon"; 
+    const std::string resName = "Argon";
     const std::vector<std::string> typeNames = {"Ar"};
 };
 
@@ -133,12 +132,19 @@ void LJ(Config& config)
     auto subdomain = data::Subdomain({-config.Lx, -config.Ly, -config.Lz},
                                      {config.Lx, config.Ly, config.Lz},
                                      config.neighborCutoff);
-    const auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
+    const auto volume = subdomain.getVolume();
     auto atoms = fillDomainWithAtomsSC(subdomain, config.numAtoms, 1_r);
     auto rho = real_c(atoms.numLocalAtoms) / volume;
     std::cout << "rho: " << rho << std::endl;
 
-    io::dumpGRO("atoms_initial.gro", atoms, subdomain, 0_r, "Argon", config.resName, config.typeNames, false);
+    io::dumpGRO("atoms_initial.gro",
+                atoms,
+                subdomain,
+                0_r,
+                "Argon",
+                config.resName,
+                config.typeNames,
+                false);
 
     communication::GhostLayer ghostLayer;
     action::LennardJones LJ(config.rc, config.sigma, config.epsilon, 0.7_r * config.sigma);

examples/LennardJones/LennardJones.cpp

@@ -1,11 +1,11 @@
 // Copyright 2024 Sebastian Eibl
-// 
+//
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
 // You may obtain a copy of the License at
-// 
+//
 //     https://www.apache.org/licenses/LICENSE-2.0
-// 
+//
 // Unless required by applicable law or agreed to in writing, software
 // distributed under the License is distributed on an "AS IS" BASIS,
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -101,7 +101,7 @@ void LJ(Config& config)
 {
     auto subdomain =
         data::Subdomain({0_r, 0_r, 0_r}, {config.Lx, config.Lx, config.Lx}, config.neighborCutoff);
-    const auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
+    const auto volume = subdomain.getVolume();
     data::Atoms atoms(0);
 
     if (!config.filename.empty())

examples/SPC/SPC.cpp

@@ -1,11 +1,11 @@
 // Copyright 2024 Sebastian Eibl
-// 
+//
 // Licensed under the Apache License, Version 2.0 (the "License");
 // you may not use this file except in compliance with the License.
 // You may obtain a copy of the License at
-// 
+//
 //     https://www.apache.org/licenses/LICENSE-2.0
-// 
+//
 // Unless required by applicable law or agreed to in writing, software
 // distributed under the License is distributed on an "AS IS" BASIS,
 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -14,12 +14,11 @@
 
 #include "action/SPC.hpp"
 
-#include <format>
-
 #include <CLI/App.hpp>
 #include <CLI/Config.hpp>
 #include <CLI/Formatter.hpp>
 #include <Kokkos_Core.hpp>
+#include <format>
 #include <fstream>
 #include <iomanip>
 #include <iostream>
@@ -191,7 +190,7 @@ void initMolecules(data::Molecules& molecules,
 void SPC(Config& config)
 {
     auto subdomain = data::Subdomain({0_r, 0_r, 0_r}, {5_r, 5_r, 5_r}, config.neighborCutoff);
-    const auto volume = subdomain.diameter[0] * subdomain.diameter[1] * subdomain.diameter[2];
+    const auto volume = subdomain.getVolume();
 
     data::Atoms atoms(0);
     data::Molecules molecules(0);
@@ -363,25 +362,25 @@ void SPC(Config& config)
         if (config.bOutput && (step > config.nsteps - 5000) && (step % 100 == 0))
         {
             io::dumpCSV(std::format("spc_{:0>6}.csv", step), atoms, false);
-            //io::dumpGRO(std::format("spc_{:0>6}.gro", step),
-            //            atoms,
-            //            subdomain,
-            //            step * config.dt,
-            //            "SPC water",
-            //            false,
-            //            true);
+            // io::dumpGRO(std::format("spc_{:0>6}.gro", step),
+            //             atoms,
+            //             subdomain,
+            //             step * config.dt,
+            //             "SPC water",
+            //             false,
+            //             true);
         }
 
         if (config.bOutput && (step > config.nsteps - 500) && (step % 10 == 0))
         {
             io::dumpCSV(std::format("spc_{:0>6}.csv", step), atoms, false);
-            //io::dumpGRO(std::format("spc_{:0>6}.gro", step),
-            //            atoms,
-            //            subdomain,
-            //            step * config.dt,
-            //            "SPC water",
-            //            false,
-            //            true);
+            // io::dumpGRO(std::format("spc_{:0>6}.gro", step),
+            //             atoms,
+            //             subdomain,
+            //             step * config.dt,
+            //             "SPC water",
+            //             false,
+            //             true);
         }
 
         if (step == 2000) config.thermostatInterval = 2000;