Merge pull request #1824 from ghutchis/xyz-precision

Add decimal precision as per forum debate (10 decimals)
OpenChemistry · Nov 29, 2024 · 1815c9d · 1815c9d
2 parents ab85ccd + f94d30d
commit 1815c9d
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Showing 2 changed files with 26 additions and 20 deletions.
diff --git a/avogadro/io/xyzformat.cpp b/avogadro/io/xyzformat.cpp
@@ -326,12 +326,12 @@ bool XyzFormat::write(std::ostream& outStream, const Core::Molecule& mol)
     }
 
     outStream << std::setw(3) << std::left
-              << Elements::symbol(atom.atomicNumber()) << " " << std::setw(10)
-              << std::right << std::fixed << std::setprecision(5)
-              << atom.position3d().x() << " " << std::setw(10) << std::right
-              << std::fixed << std::setprecision(5) << atom.position3d().y()
-              << " " << std::setw(10) << std::right << std::fixed
-              << std::setprecision(5) << atom.position3d().z() << "\n";
+              << Elements::symbol(atom.atomicNumber()) << " " << std::setw(15)
+              << std::right << std::fixed << std::setprecision(10)
+              << atom.position3d().x() << " " << std::setw(15) << std::right
+              << std::fixed << std::setprecision(10) << atom.position3d().y()
+              << " " << std::setw(15) << std::right << std::fixed
+              << std::setprecision(10) << atom.position3d().z() << "\n";
   }
 
   return true;

diff --git a/tests/io/xyztest.cpp b/tests/io/xyztest.cpp
@@ -28,11 +28,11 @@
 #include <sstream>
 #include <string>
 
+using Avogadro::Vector3;
 using Avogadro::Core::Atom;
 using Avogadro::Core::Molecule;
 using Avogadro::Io::FileFormat;
 using Avogadro::Io::XyzFormat;
-using Avogadro::Vector3;
 
 // methane.xyz uses atomic symbols to identify atoms
 TEST(XyzTest, readAtomicSymbols)
@@ -119,19 +119,25 @@ TEST(XyzTest, write)
   std::string output;
   EXPECT_EQ(xyz.writeString(output, molecule), true);
 
-  // The output should be an exact match with the sample file.
-  std::istringstream outputStream(output);
-  std::ifstream refStream(AVOGADRO_DATA "/data/methane.xyz");
-  char outputChar = '\0';
-  char refChar = '\0';
-  outputStream >> std::noskipws;
-  refStream >> std::noskipws;
-  bool checkedSomething = false;
-  while ((outputStream >> outputChar) && (refStream >> refChar)) {
-    ASSERT_EQ(refChar, outputChar);
-    checkedSomething = true;
-  }
-  EXPECT_TRUE(checkedSomething);
+  // this part is more of a roundtrip test
+  Molecule readMolecule;
+  xyz.readString(output, readMolecule);
+
+  // make sure we've got the same thing
+  EXPECT_EQ(readMolecule.atomCount(), 5);
+
+  // Bond perception will result in 4 bonds
+  EXPECT_EQ(readMolecule.bondCount(), 4);
+
+  EXPECT_EQ(readMolecule.atom(0).atomicNumber(), 6);
+  EXPECT_EQ(readMolecule.atom(1).atomicNumber(), 1);
+  EXPECT_EQ(readMolecule.atom(2).atomicNumber(), 1);
+  EXPECT_EQ(readMolecule.atom(3).atomicNumber(), 1);
+  EXPECT_EQ(readMolecule.atom(4).atomicNumber(), 1);
+
+  EXPECT_EQ(readMolecule.atom(4).position3d().x(), -0.51336);
+  EXPECT_EQ(readMolecule.atom(4).position3d().y(), 0.889165);
+  EXPECT_EQ(readMolecule.atom(4).position3d().z(), -0.36300);
 }
 
 TEST(XyzTest, modes)