Merge pull request #603 from ghutchis/read-extended-xyz

Transparent support for ASE "extended XYZ" files

avogadro/io/xyzformat.cpp

@@ -1,23 +1,13 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2013 Kitware, Inc.
-
-  This source code is released under the New BSD License, (the "License").
-
-  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.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include "xyzformat.h"
 
 #include <avogadro/core/elements.h>
 #include <avogadro/core/molecule.h>
+#include <avogadro/core/unitcell.h>
 #include <avogadro/core/utilities.h>
 #include <avogadro/core/vector.h>
 
@@ -31,10 +21,10 @@
 
 using json = nlohmann::json;
 
-using std::string;
 using std::endl;
 using std::getline;
 using std::string;
+using std::string;
 using std::vector;
 
 namespace Avogadro {
@@ -52,13 +42,9 @@ using Core::trimmed;
 using std::isalpha;
 #endif
 
-XyzFormat::XyzFormat()
-{
-}
+XyzFormat::XyzFormat() {}
 
-XyzFormat::~XyzFormat()
-{
-}
+XyzFormat::~XyzFormat() {}
 
 bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
 {
@@ -80,6 +66,31 @@ bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
   if (!buffer.empty())
     mol.setData("name", trimmed(buffer));
 
+  // check for Lattice= in an extended XYZ from ASE and company
+  // e.g. Lattice="H11 H21 H31 H12 H22 H32 H13 H23 H33"
+  // https://atomsk.univ-lille.fr/doc/en/format_xyz.html
+  // https://gitlab.com/ase/ase/-/merge_requests/62
+  std::size_t start = buffer.find("Lattice=\"");
+  if (start != std::string::npos) {
+    // step through bit by bit until we hit the next quote character
+    start = start + 9;
+    std::size_t end = buffer.find('\"', start);
+    std::string lattice = buffer.substr(start, (end - start));
+
+    vector<string> tokens(split(lattice, ' '));
+    if (tokens.size() == 9) {
+      Vector3 v1(lexicalCast<double>(tokens[0]), lexicalCast<double>(tokens[1]),
+                 lexicalCast<double>(tokens[2]));
+      Vector3 v2(lexicalCast<double>(tokens[3]), lexicalCast<double>(tokens[4]),
+                 lexicalCast<double>(tokens[5]));
+      Vector3 v3(lexicalCast<double>(tokens[6]), lexicalCast<double>(tokens[7]),
+                 lexicalCast<double>(tokens[8]));
+
+      Core::UnitCell* cell = new Core::UnitCell(v1, v2, v3);
+      mol.setUnitCell(cell);
+    }
+  }
+
   // Parse atoms
   for (size_t i = 0; i < numAtoms; ++i) {
     getline(inStream, buffer);
@@ -162,10 +173,31 @@ bool XyzFormat::write(std::ostream& outStream, const Core::Molecule& mol)
   size_t numAtoms = mol.atomCount();
 
   outStream << numAtoms << std::endl;
-  if (mol.data("name").toString().length())
-    outStream << mol.data("name").toString() << endl;
-  else
-    outStream << "XYZ file generated by Avogadro.\n";
+
+  if (mol.unitCell()) {
+    // default to including Lattice for extended XYZ if present
+    // https://atomsk.univ-lille.fr/doc/en/format_xyz.html
+    // https://gitlab.com/ase/ase/-/merge_requests/62
+    outStream << "Lattice=\"";
+    outStream << mol.unitCell()->aVector().x() << ' ';
+    outStream << mol.unitCell()->aVector().y() << ' ';
+    outStream << mol.unitCell()->aVector().z() << ' ';
+
+    outStream << mol.unitCell()->bVector().x() << ' ';
+    outStream << mol.unitCell()->bVector().y() << ' ';
+    outStream << mol.unitCell()->bVector().z() << ' ';
+
+    outStream << mol.unitCell()->cVector().x() << ' ';
+    outStream << mol.unitCell()->cVector().y() << ' ';
+    outStream << mol.unitCell()->cVector().z();
+
+    outStream << "\" Properties=species:S:1:pos:R:3" << endl;
+  } else {
+    if (mol.data("name").toString().length())
+      outStream << mol.data("name").toString() << endl;
+    else
+      outStream << "XYZ file generated by Avogadro.\n";
+  }
 
   for (size_t i = 0; i < numAtoms; ++i) {
     Atom atom = mol.atom(i);
@@ -190,6 +222,7 @@ std::vector<std::string> XyzFormat::fileExtensions() const
 {
   std::vector<std::string> ext;
   ext.push_back("xyz");
+  ext.push_back("extxyz");
   return ext;
 }
 
@@ -200,5 +233,5 @@ std::vector<std::string> XyzFormat::mimeTypes() const
   return mime;
 }
 
-} // end Io namespace
-} // end Avogadro namespace
+} // namespace Io
+} // namespace Avogadro

avogadro/io/xyzformat.h

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2013 Kitware, Inc.
-
-  This source code is released under the New BSD License, (the "License").
-
-  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.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #ifndef AVOGADRO_IO_XYZFORMAT_H