diff --git a/include/tadah/mlip/structure.h b/include/tadah/mlip/structure.h
index 47ef531c2c3f15a6c248c62fed815e3496d3b869..439bb3588e12954939bc044d678b8732831ca045 100644
--- a/include/tadah/mlip/structure.h
+++ b/include/tadah/mlip/structure.h
@@ -3,6 +3,7 @@
#include <tadah/mlip/atom.h>
#include <tadah/core/core_types.h>
+#include <tadah/core/periodic_table.h>
#include <string>
#include <iostream>
diff --git a/src/structure_db.cpp b/src/structure_db.cpp
index 9f31fb60bcee4420295d982b5cfc9ad02124ce8f..f47b5e5e035015b94ddad6d9a2e28a5d3214daa0 100644
--- a/src/structure_db.cpp
+++ b/src/structure_db.cpp
@@ -108,37 +108,34 @@ std::set<Element> StructureDB::get_unique_elements() const {
}
std::set<Element> StructureDB::find_unique_elements(const std::string &fn) {
std::set<Element> s;
- std::ifstream datafile(fn);
+ std::ifstream ifs(fn);
std::string line;
- if (!datafile.is_open()) {
+ if (!ifs.is_open()) {
std::cerr << "Could not open the file." << std::endl;
}
char symbol[3];
-
- // move to first non empty line
- while (std::getline(datafile, line)) {
- if (!line.empty()) {
- break;
- }
- }
- // skip
- for (int i = 0; i < 7; ++i) {
- std::getline(datafile, line);
- }
- while (std::getline(datafile, line)) {
- if(line.empty()) {
- for (int i = 0; i < 8; ++i) {
- if (!std::getline(datafile, line)) {
- // Handle the case where there are not enough lines
- break; // or handle the error
- }
- }
- continue;
+ while (std::getline(ifs, line)) {
+ // the second line could be energy or
+ // a scalling factors eweight fweight sweight
+ std::getline(ifs,line);
+ std::stringstream stream(line);
+ size_t count = std::distance(std::istream_iterator<std::string>(stream),
+ std::istream_iterator<std::string>());
+
+ if (count == 3)
+ std::getline(ifs,line);
+
+ for (size_t i=0; i<6; ++i)
+ std::getline(ifs,line);
+
+ while (std::getline(ifs, line)) {
+ if(line.empty()) break;
+ sscanf(line.c_str(), "%2s", symbol);
+ s.insert(PeriodicTable::find_by_symbol(symbol));
}
- sscanf(line.c_str(), "%2s", symbol);
- s.insert(PeriodicTable::find_by_symbol(symbol));
+
}
return s;
}
diff --git a/tests/test_structure.cpp b/tests/test_structure.cpp
index 39c3489e1d5850d2c6c210c3e13d60d683186463..1a0292c725f931e458256a6f5717bd6b58ead8a5 100644
--- a/tests/test_structure.cpp
+++ b/tests/test_structure.cpp
@@ -7,112 +7,116 @@
// Conversion factor from eV/A^3 to kbar;
double fac = 1602.1766208;
+
TEST_CASE( "Testing Structure class volume", "[structure_volume]" ) {
- //using vec=Eigen::Vector3d;
+ //using vec=Eigen::Vector3d;
- //std::string symbol="Ti";
- //std::string name="Titanium";
- //int Z = 22;
- //vec pos(1.0,2.0,3.0);
- //vec force(4.0,5.0,6.0);
- //Element element(symbol,name,Z);
+ //std::string symbol="Ti";
+ //std::string name="Titanium";
+ //int Z = 22;
+ //vec pos(1.0,2.0,3.0);
+ //vec force(4.0,5.0,6.0);
+ //Element element(symbol,name,Z);
- //Atom a(element, 1.0, 2.0, 3.0,
- // 4.0, 5.0, 6.0);
+ //Atom a(element, 1.0, 2.0, 3.0,
+ // 4.0, 5.0, 6.0);
- Structure st;
- // Integer volume
- st.cell.load(2,-1,3,
- 3,2,-4,
- -2,0,1);
+ Structure st;
+ // Integer volume
+ st.cell.load(2,-1,3,
+ 3,2,-4,
+ -2,0,1);
- REQUIRE(st.get_volume() == 11 );
+ REQUIRE(st.get_volume() == 11 );
- // double volume
- st.cell.load(5.0147,5.0104,-5.0018,
- -9.9924,-3.3395,-9.9662,
- -25.6396,38.4594,12.8198);
+ // double volume
+ st.cell.load(5.0147,5.0104,-5.0018,
+ -9.9924,-3.3395,-9.9662,
+ -25.6396,38.4594,12.8198);
- REQUIRE(st.get_volume() == Approx(5980.0279772134).epsilon(1e-10));
+ REQUIRE(st.get_volume() == Approx(5980.0279772134).epsilon(1e-10));
}
TEST_CASE( "Testing Structure virial pressure calculations", "[structure_virial_pressures]" ) {
- Structure st;
- st.cell.load(9.374769,0.0,0.0,
- 0.0,9.374769,0.0,
- 0.0,0.0,9.374769);
+ Structure st;
+ st.cell.load(9.374769,0.0,0.0,
+ 0.0,9.374769,0.0,
+ 0.0,0.0,9.374769);
- REQUIRE(st.get_volume() == Approx(823.91));
+ REQUIRE(st.get_volume() == Approx(823.91));
- st.stress.load(257.0893807653,0.0,0.0,
- 0.0,257.0893807653,0.0,
- 0.0,0.0,257.0893807653);
- REQUIRE(fac*st.get_virial_pressure() == Approx(499.93));
+ st.stress.load(257.0893807653,0.0,0.0,
+ 0.0,257.0893807653,0.0,
+ 0.0,0.0,257.0893807653);
+ REQUIRE(fac*st.get_virial_pressure() == Approx(499.93));
}
TEST_CASE( "Testing Structure read and write", "[structure_read_write]" ) {
- Structure st;
- st.read("tests_data/structure_1.dat");
+ PeriodicTable::initialize();
+ Structure st;
+ st.read("tests_data/structure_1.dat");
- REQUIRE(st.get_volume() == Approx(989.521812));
+ REQUIRE(st.get_volume() == Approx(989.521812));
- REQUIRE(fac*st.get_virial_pressure() == Approx(26.705578));
- REQUIRE(fac*st.get_pressure(300) == Approx(28.965914));
- REQUIRE(fac*st.get_pressure(0) == Approx(26.705578));
+ REQUIRE(fac*st.get_virial_pressure() == Approx(26.705578));
+ REQUIRE(fac*st.get_pressure(300) == Approx(28.965914));
+ REQUIRE(fac*st.get_pressure(0) == Approx(26.705578));
- std::string tempfile = std::tmpnam(nullptr);
- st.save(tempfile);
+ std::string tempfile = std::tmpnam(nullptr);
+ st.save(tempfile);
- Structure st_temp;
- st_temp.read(tempfile);
+ Structure st_temp;
+ st_temp.read(tempfile);
- REQUIRE(st_temp.get_volume() == Approx(989.521812));
+ REQUIRE(st_temp.get_volume() == Approx(989.521812));
- REQUIRE(fac*st_temp.get_virial_pressure() == Approx(26.705578));
- REQUIRE(fac*st_temp.get_pressure(300) == Approx(28.965914));
- REQUIRE(fac*st_temp.get_pressure(0) == Approx(26.705578));
+ REQUIRE(fac*st_temp.get_virial_pressure() == Approx(26.705578));
+ REQUIRE(fac*st_temp.get_pressure(300) == Approx(28.965914));
+ REQUIRE(fac*st_temp.get_pressure(0) == Approx(26.705578));
- REQUIRE(st==st_temp);
+ REQUIRE(st==st_temp);
- std::remove(tempfile.c_str());
+ std::remove(tempfile.c_str());
}
TEST_CASE( "Testing Structure compare", "[structure_compare]" ) {
- Structure st;
- st.read("tests_data/structure_1.dat");
- std::string tempfile = std::tmpnam(nullptr);
- st.save(tempfile);
-
- Structure st_temp;
- st_temp.read(tempfile);
-
- SECTION("Compare unchanged") {
- REQUIRE(st==st_temp);
- }
- SECTION("Compare symbols") {
- REQUIRE(st==st_temp);
- st_temp.atoms[0].symbol[0]='X';
- st_temp.atoms[0].symbol[1]='X';
- REQUIRE(!(st==st_temp));
- }
- SECTION("Compare position") {
- REQUIRE(st==st_temp);
- st_temp.atoms[0].position(0.12,0.13,10.14);
- REQUIRE(!(st==st_temp));
- }
- SECTION("Compare force") {
- REQUIRE(st==st_temp);
- st_temp.atoms[0].force(1.12, 0.13, 0.134);
- REQUIRE(!(st==st_temp));
- }
-
- std::remove(tempfile.c_str());
+ PeriodicTable::initialize();
+ Structure st;
+ st.read("tests_data/structure_1.dat");
+ std::string tempfile = std::tmpnam(nullptr);
+ st.save(tempfile);
+
+ Structure st_temp;
+ st_temp.read(tempfile);
+
+ SECTION("Compare unchanged") {
+ REQUIRE(st==st_temp);
+ }
+ SECTION("Compare symbols") {
+ REQUIRE(st==st_temp);
+ st_temp.atoms[0].symbol[0]='X';
+ st_temp.atoms[0].symbol[1]='X';
+ REQUIRE(!(st==st_temp));
+ }
+ SECTION("Compare position") {
+ REQUIRE(st==st_temp);
+ st_temp.atoms[0].position(0.12,0.13,10.14);
+ REQUIRE(!(st==st_temp));
+ }
+ SECTION("Compare force") {
+ REQUIRE(st==st_temp);
+ st_temp.atoms[0].force(1.12, 0.13, 0.134);
+ REQUIRE(!(st==st_temp));
+ }
+
+ std::remove(tempfile.c_str());
}
TEST_CASE( "Testing Structure copy", "[structure_copy]" ) {
- Structure st;
- st.read("tests_data/structure_1.dat");
- Structure st2=st;
- REQUIRE(st==st2);
+ PeriodicTable::initialize();
+ Structure st;
+ st.read("tests_data/structure_1.dat");
+ Structure st2=st;
+ REQUIRE(st==st2);
}