Fix radii print out + add two new solvents

Author: Roberto Di Remigio

CHANGELOG.md

@@ -161,6 +161,10 @@
 
 ## v1.0.0 (2014-09-30) [YANKED]
 
-[Unreleased]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.1...HEAD
+[Unreleased]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.5...HEAD
+[v1.1.5]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.4...v1.1.5
+[v1.1.4]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.3...v1.1.4
+[v1.1.3]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.2...v1.1.3
+[v1.1.2]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.1...v1.1.3
 [v1.1.1]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.0...v1.1.1
 [v1.1.0]: https://github.com/PCMSolver/pcmsolver/releases/tag/v1.1.0

doc/users/input.rst

@@ -47,6 +47,21 @@ Available sections:
 + Green, subsection of medium. Sets up the Green's function inside and
   outside the cavity.
 
+.. warning::
+
+   Exactly matching results obtained from implementations of IEFPCM and/or
+   CPCM (COSMO) given in other program packages requires careful selection of
+   all the parameters involved.
+   A partial checklist of parameters you should always keep in mind:
+
+   * solvent permittivities (static and optical)
+   * atomic radii set
+   * scaling of the atomic radii
+   * cavity surface
+   * cavity partition (tesselation)
+   * PCM matrix formation algorithm
+   * strategy used to solve the PCM linear equations system.
+
 Top section keywords
 --------------------
 
@@ -110,7 +125,7 @@ Cavity section keywords
    RadiiSet
      Select set of atomic radii to be used. Currently Bondi-Mantina
      :cite:`Bondi1964,Mantina2009`, UFF :cite:`Rappe1992` and Allinger's MM3
-     :cite`Allinger1994-tx` sets available, see :ref:`available-radii`.
+     :cite:`Allinger1994-tx` sets available, see :ref:`available-radii`.
 
      * **Type**: string
      * **Valid values**: Bondi | UFF | Allinger
@@ -120,7 +135,7 @@ Cavity section keywords
      .. note::
 
         Radii in Allinger's MM3 set are obtained by **dividing** the value in the original
-        paper by 1.2, as done in the [ADF COSMO implementation](https://www.scm.com/doc/ADF/Input/COSMO.html)
+        paper by 1.2, as done in the `ADF COSMO implementation <https://www.scm.com/doc/ADF/Input/COSMO.html>`_
         We advise to turn off scaling of the radii by 1.2 when using this set.
 
    MinRadius
@@ -210,24 +225,26 @@ Medium section keywords
      * **Type**: string
      * **Valid values**:
 
-        + Water               , H2O;
-        + Methanol            , CH3OH;
-        + Ethanol             , CH3CH2OH;
-        + Chloroform          , CHCL3;
-        + Methylenechloride   , CH2CL2;
-        + 1,2-Dichloroethane  , C2H4CL2;
-        + Carbon Tetrachloride, CCL4;
-        + Benzene             , C6H6;
-        + Toluene             , C6H5CH3;
-        + Chlorobenzene       , C6H5CL;
-        + Nitromethane        , CH3NO2;
-        + N-heptane           , C7H16;
-        + Cyclohexane         , C6H12;
-        + Aniline             , C6H5NH2;
-        + Acetone             , C2H6CO;
-        + Tetrahydrofurane    , THF;
-        + Dimethylsulfoxide   , DMSO;
-        + Acetonitrile        , CH3CN;
+        + Water                , H2O;
+        + Propylene Carbonate  , C4H6O3;
+        + Dimethylsulfoxide    , DMSO;
+        + Nitromethane         , CH3NO2;
+        + Acetonitrile         , CH3CN;
+        + Methanol             , CH3OH;
+        + Ethanol              , CH3CH2OH;
+        + Acetone              , C2H6CO;
+        + 1,2-Dichloroethane   , C2H4CL2;
+        + Methylenechloride    , CH2CL2;
+        + Tetrahydrofurane     , THF;
+        + Aniline              , C6H5NH2;
+        + Chlorobenzene        , C6H5CL;
+        + Chloroform           , CHCL3;
+        + Toluene              , C6H5CH3;
+        + 1,4-Dioxane          , C4H8O2;
+        + Benzene              , C6H6;
+        + Carbon Tetrachloride , CCL4;
+        + Cyclohexane          , C6H12;
+        + N-heptane            , C7H16;
         + Explicit.
 
    MatrixSymm
@@ -454,6 +471,7 @@ Solvents are ordered by decreasing static permittivity.
  Name                 Formula  :math:`\varepsilon_s` :math:`\varepsilon_\infty` :math:`r_\mathrm{probe}`
  ==================== ======== ===================== ========================== ========================
  Water                H2O              78.39                 1.776                     1.385
+ Propylene Carbonate  C4H6O3           64.96                 2.019                     1.385
  Dimethylsulfoxide    DMSO             46.7                  2.179                     2.455
  Nitromethane         CH3NO2           38.20                 1.904                     2.155
  Acetonitrile         CH3CN            36.64                 1.806                     2.155
@@ -467,6 +485,7 @@ Solvents are ordered by decreasing static permittivity.
  Chlorobenzene        C6H5Cl            5.621                2.320                     2.805
  Chloroform           CHCl3             4.90                 2.085                     2.48
  Toluene              C6H5CH3           2.379                2.232                     2.82
+ 1,4-Dioxane          C4H8O2            2.250                2.023                     2.630
  Benzene              C6H6              2.247                2.244                     2.630
  Carbon tetrachloride CCl4              2.228                2.129                     2.685
  Cyclohexane          C6H12             2.023                2.028                     2.815

src/bin/run_pcm.cpp

@@ -2,22 +2,22 @@
 /*
  *     PCMSolver, an API for the Polarizable Continuum Model
  *     Copyright (C) 2013-2016 Roberto Di Remigio, Luca Frediani and contributors
- *     
+ *
  *     This file is part of PCMSolver.
- *     
+ *
  *     PCMSolver is free software: you can redistribute it and/or modify
  *     it under the terms of the GNU Lesser General Public License as published by
  *     the Free Software Foundation, either version 3 of the License, or
  *     (at your option) any later version.
- *     
+ *
  *     PCMSolver is distributed in the hope that it will be useful,
  *     but WITHOUT ANY WARRANTY; without even the implied warranty of
  *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *     GNU Lesser General Public License for more details.
- *     
+ *
  *     You should have received a copy of the GNU Lesser General Public License
  *     along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
- *     
+ *
  *     For information on the complete list of contributors to the
  *     PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
  */
@@ -105,6 +105,7 @@ int main(int argc, char * argv[])
     out_stream << "Using CODATA " << parsed.CODATAyear() << " set of constants." << std::endl;
     out_stream << "Input parsing done " << parsed.providedBy() << std::endl;
     out_stream << "========== Cavity " << std::endl;
+    out_stream << "Atomic radii set: " << parsed.radiiSetName() << std::endl;
     out_stream << *cavity << std::endl;
     out_stream << "========== Solver " << std::endl;
     out_stream << *solver << std::endl;

src/interface/Input.cpp

@@ -2,22 +2,22 @@
 /*
  *     PCMSolver, an API for the Polarizable Continuum Model
  *     Copyright (C) 2013-2016 Roberto Di Remigio, Luca Frediani and contributors
- *     
+ *
  *     This file is part of PCMSolver.
- *     
+ *
  *     PCMSolver is free software: you can redistribute it and/or modify
  *     it under the terms of the GNU Lesser General Public License as published by
  *     the Free Software Foundation, either version 3 of the License, or
  *     (at your option) any later version.
- *     
+ *
  *     PCMSolver is distributed in the hope that it will be useful,
  *     but WITHOUT ANY WARRANTY; without even the implied warranty of
  *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *     GNU Lesser General Public License for more details.
- *     
+ *
  *     You should have received a copy of the GNU Lesser General Public License
  *     along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
- *     
+ *
  *     For information on the complete list of contributors to the
  *     PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
  */
@@ -274,23 +274,30 @@ void Input::initMolecule()
   }
   // 3. list of atoms and list of spheres
   double factor = angstromToBohr();
-  std::vector<Atom> radiiSet, atoms;
+  std::vector<Atom> radiiSet;
+  std::vector<Atom> atoms;
   if ( radiiSet_ == "UFF" ) {
     radiiSet = initUFF();
-  } else {
+    radiiSetName_ = "UFF";
+  } else if ( radiiSet_ == "BONDI" ) {
     radiiSet = initBondi();
+    radiiSetName_ = "Bondi-Mantina";
+  } else {
+    radiiSet = initAllinger();
+    radiiSetName_ = "Allinger's MM3";
   }
   for (int i = 0; i < charges.size(); ++i) {
     int index = int(charges(i)) - 1;
     atoms.push_back(radiiSet[index]);
+    if (scaling_) atoms[index].radiusScaling = 1.2;
   }
   // Based on the creation mode (Implicit or Atoms)
   // the spheres list might need postprocessing
   if ( mode_ == "IMPLICIT" || mode_ == "ATOMS") {
     for (int i = 0; i < charges.size(); ++i) {
       int index = int(charges(i)) - 1;
       double radius = radiiSet[index].radius * factor;
-      if (scaling_) radius *= radiiSet[index].radiusScaling;
+      if (scaling_) radius *= 1.2;
       spheres_.push_back(Sphere(centers.col(i), radius));
     }
     if (mode_ == "ATOMS") {

src/interface/Input.hpp

@@ -2,22 +2,22 @@
 /*
  *     PCMSolver, an API for the Polarizable Continuum Model
  *     Copyright (C) 2013-2016 Roberto Di Remigio, Luca Frediani and contributors
- *     
+ *
  *     This file is part of PCMSolver.
- *     
+ *
  *     PCMSolver is free software: you can redistribute it and/or modify
  *     it under the terms of the GNU Lesser General Public License as published by
  *     the Free Software Foundation, either version 3 of the License, or
  *     (at your option) any later version.
- *     
+ *
  *     PCMSolver is distributed in the hope that it will be useful,
  *     but WITHOUT ANY WARRANTY; without even the implied warranty of
  *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *     GNU Lesser General Public License for more details.
- *     
+ *
  *     You should have received a copy of the GNU Lesser General Public License
  *     along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
- *     
+ *
  *     For information on the complete list of contributors to the
  *     PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
  */
@@ -78,6 +78,7 @@ class Input
     std::string cavityType() const { return type_; }
     bool scaling() const { return scaling_; }
     std::string radiiSet() const { return radiiSet_; }
+    std::string radiiSetName() const { return radiiSetName_; }
     std::string mode() const { return mode_; }
     std::vector<int> atoms() const { return atoms_; }
     int atoms(size_t i) const { return atoms_[i]; }
@@ -165,6 +166,8 @@ class Input
     bool scaling_;
     /// The set of radii to be used
     std::string radiiSet_;
+    /// Collects info on atomic radii set
+    std::string radiiSetName_;
     /// Minimal radius of an added sphere
     double minimalRadius_;
     /// How the API should get the coordinates of the sphere centers

src/interface/Meddle.cpp

@@ -2,22 +2,22 @@
 /*
  *     PCMSolver, an API for the Polarizable Continuum Model
  *     Copyright (C) 2013-2016 Roberto Di Remigio, Luca Frediani and contributors
- *     
+ *
  *     This file is part of PCMSolver.
- *     
+ *
  *     PCMSolver is free software: you can redistribute it and/or modify
  *     it under the terms of the GNU Lesser General Public License as published by
  *     the Free Software Foundation, either version 3 of the License, or
  *     (at your option) any later version.
- *     
+ *
  *     PCMSolver is distributed in the hope that it will be useful,
  *     but WITHOUT ANY WARRANTY; without even the implied warranty of
  *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *     GNU Lesser General Public License for more details.
- *     
+ *
  *     You should have received a copy of the GNU Lesser General Public License
  *     along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
- *     
+ *
  *     For information on the complete list of contributors to the
  *     PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
  */
@@ -178,6 +178,7 @@ namespace pcm {
   {
     TIMER_ON("Meddle::initInput");
     initInput(input_reading, nr_nuclei, charges, coordinates, symmetry_info, host_input);
+    radiiSetName_ = input_.radiiSetName();
     TIMER_OFF("Meddle::initInput");
 
     TIMER_ON("Meddle::initCavity");
@@ -378,6 +379,7 @@ namespace pcm {
     cavity_->saveCavity();
 
     infoStream_ << "========== Cavity " << std::endl;
+    infoStream_ << "Atomic radii set: " << radiiSetName_ << std::endl;
     infoStream_ << *cavity_;
   }
 
@@ -458,20 +460,22 @@ namespace pcm {
     bool scaling = inp.scaling();
     std::string set = inp.radiiSet();
     double factor = angstromToBohr();
-    std::vector<Atom> radiiSet, atoms;
+    std::vector<Atom> radiiSet;
+    std::vector<Atom> atoms;
     if ( set == "UFF" ) {
       radiiSet = initUFF();
-    } else {
+    } else if ( set == "BONDI" ) {
       radiiSet = initBondi();
+    } else {
+      radiiSet = initAllinger();
     }
     std::vector<Sphere> spheres;
     for (int i = 0; i < charges.size(); ++i) {
       int index = int(charges(i)) - 1;
       atoms.push_back(radiiSet[index]);
+      if (scaling) atoms[index].radiusScaling = 1.2;
       double radius = radiiSet[index].radius * factor;
-      if (scaling) {
-        radius *= radiiSet[index].radiusScaling;
-      }
+      if (scaling) radius *= 1.2;
       spheres.push_back(Sphere(centers.col(i), radius));
     }
     Eigen::VectorXd masses = Eigen::VectorXd::Zero(nuclei);

src/interface/Meddle.hpp

@@ -2,22 +2,22 @@
 /*
  *     PCMSolver, an API for the Polarizable Continuum Model
  *     Copyright (C) 2013-2016 Roberto Di Remigio, Luca Frediani and contributors
- *     
+ *
  *     This file is part of PCMSolver.
- *     
+ *
  *     PCMSolver is free software: you can redistribute it and/or modify
  *     it under the terms of the GNU Lesser General Public License as published by
  *     the Free Software Foundation, either version 3 of the License, or
  *     (at your option) any later version.
- *     
+ *
  *     PCMSolver is distributed in the hope that it will be useful,
  *     but WITHOUT ANY WARRANTY; without even the implied warranty of
  *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *     GNU Lesser General Public License for more details.
- *     
+ *
  *     You should have received a copy of the GNU Lesser General Public License
  *     along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
- *     
+ *
  *     For information on the complete list of contributors to the
  *     PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
  */
@@ -174,6 +174,8 @@ namespace pcm {
             bool hasDynamic_;
             /*! SurfaceFunction map */
             mutable SurfaceFunctionMap functions_;
+            /*! Collects info on atomic radii set */
+            std::string radiiSetName_;
             /*! Initialize input_ */
             void initInput(pcmsolver_reader_t input_reading, int nr_nuclei, double charges[], double coordinates[], int symmetry_info[], const PCMInput & host_input);
             /*! Initialize cavity_ */