From 81e181ae44c9343b0772a8f064d007df23a8e35a Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Tue, 26 Nov 2024 12:26:35 +0000
Subject: [PATCH 1/3] new add method
---
include/tadah/mlip/st_descriptors_db.h | 19 +++++++++++--------
src/st_descriptors_db.cpp | 3 +++
2 files changed, 14 insertions(+), 8 deletions(-)
diff --git a/include/tadah/mlip/st_descriptors_db.h b/include/tadah/mlip/st_descriptors_db.h
index db8843c..7f45999 100644
--- a/include/tadah/mlip/st_descriptors_db.h
+++ b/include/tadah/mlip/st_descriptors_db.h
@@ -15,25 +15,28 @@
*
*/
struct StDescriptorsDB {
- std::vector<StDescriptors> st_descs;
- StDescriptorsDB() {};
+ std::vector<StDescriptors> st_descs;
+ StDescriptorsDB() {};
- /** This constructor fully initialise this object
+ /** This constructor fully initialise this object
*
* Requires:
* - StructureDB st to have all nearest neighbours calculated
* - Config to contain keys: \ref FORCE, \ref STRESS
* and \ref INTERNAL_KEY \ref DSIZE
*/
- StDescriptorsDB(const StructureDB &stdb, Config &config);
+ StDescriptorsDB(const StructureDB &stdb, Config &config);
- /** Return reference to the n-th StDescriptors
+ /** Return reference to the n-th StDescriptors
* stored by this object
*/
- StDescriptors& operator()(const size_t n);
+ StDescriptors& operator()(const size_t n);
- /** Return number of StDescriptors stored */
- size_t size() const;
+ /** Return number of StDescriptors stored */
+ size_t size() const;
+
+ /** Add StDescriptors to DB */
+ void add(const StDescriptors &st_d);
};
#endif
diff --git a/src/st_descriptors_db.cpp b/src/st_descriptors_db.cpp
index 9f80ce0..21960ac 100644
--- a/src/st_descriptors_db.cpp
+++ b/src/st_descriptors_db.cpp
@@ -15,3 +15,6 @@ StDescriptors &StDescriptorsDB::operator()(const size_t s) {
size_t StDescriptorsDB::size() const {
return st_descs.size();
}
+void StDescriptorsDB::add(const StDescriptors &st_d) {
+ st_descs.push_back(st_d);
+}
--
GitLab
From 9c11cfeea09d9130c79162428e20e35ab72d1e3b Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Tue, 26 Nov 2024 13:10:09 +0000
Subject: [PATCH 2/3] replaced std::tmpnam
---
tests/test_structure.cpp | 115 +++++++++++++++++++++++----------------
1 file changed, 68 insertions(+), 47 deletions(-)
diff --git a/tests/test_structure.cpp b/tests/test_structure.cpp
index 055f39a..0b890d5 100644
--- a/tests/test_structure.cpp
+++ b/tests/test_structure.cpp
@@ -56,63 +56,84 @@ TEST_CASE( "Testing Structure virial pressure calculations", "[structure_virial_
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");
+TEST_CASE("Testing Structure read and write", "[structure_read_write]") {
+ 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));
+ // Create a temporary file
+ std::FILE* tmpFile = std::tmpfile();
+ if (!tmpFile) {
+ FAIL("Unable to create temporary file");
+ }
- std::string tempfile = std::tmpnam(nullptr);
- st.save(tempfile);
+ const int fd = fileno(tmpFile);
+ REQUIRE(fd != -1);
- Structure st_temp;
- st_temp.read(tempfile);
+ char tempfile[256];
+ snprintf(tempfile, sizeof(tempfile), "/proc/self/fd/%d", fd);
- REQUIRE(st_temp.get_volume() == Approx(989.521812));
+ st.save(tempfile);
- 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));
+ Structure st_temp;
+ st_temp.read(tempfile);
- REQUIRE(st==st_temp);
+ 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));
- std::remove(tempfile.c_str());
+ REQUIRE(st == st_temp);
+ // Temporary file will be closed automatically
}
-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());
+TEST_CASE("Testing Structure compare", "[structure_compare]") {
+ Structure st;
+ st.read("tests_data/structure_1.dat");
+
+ // Create a temporary file
+ std::FILE* tmpFile = std::tmpfile();
+ if (!tmpFile) {
+ FAIL("Unable to create temporary file");
+ }
+
+ const int fd = fileno(tmpFile);
+ REQUIRE(fd != -1);
+
+ char tempfile[256];
+ snprintf(tempfile, sizeof(tempfile), "/proc/self/fd/%d", fd);
+
+ 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));
+ }
+
+ // Temporary file will be closed automatically
}
TEST_CASE( "Testing Structure copy", "[structure_copy]" ) {
Structure st;
--
GitLab
From 81a3bb2bce791926165bbc7e5f9010866deabedc Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Tue, 26 Nov 2024 13:10:39 +0000
Subject: [PATCH 3/3] Added range based loops
---
include/tadah/mlip/st_descriptors_db.h | 6 ++++++
src/st_descriptors_db.cpp | 15 +++++++++++++++
2 files changed, 21 insertions(+)
diff --git a/include/tadah/mlip/st_descriptors_db.h b/include/tadah/mlip/st_descriptors_db.h
index 7f45999..6272db8 100644
--- a/include/tadah/mlip/st_descriptors_db.h
+++ b/include/tadah/mlip/st_descriptors_db.h
@@ -38,5 +38,11 @@ struct StDescriptorsDB {
/** Add StDescriptors to DB */
void add(const StDescriptors &st_d);
+ // Methods to enable range-based for loop
+ std::vector<StDescriptors>::iterator begin();
+ std::vector<StDescriptors>::iterator end();
+ std::vector<StDescriptors>::const_iterator begin() const;
+ std::vector<StDescriptors>::const_iterator end() const;
+
};
#endif
diff --git a/src/st_descriptors_db.cpp b/src/st_descriptors_db.cpp
index 21960ac..3dce74f 100644
--- a/src/st_descriptors_db.cpp
+++ b/src/st_descriptors_db.cpp
@@ -18,3 +18,18 @@ size_t StDescriptorsDB::size() const {
void StDescriptorsDB::add(const StDescriptors &st_d) {
st_descs.push_back(st_d);
}
+std::vector<StDescriptors>::iterator StDescriptorsDB::begin() {
+ return st_descs.begin();
+}
+
+std::vector<StDescriptors>::iterator StDescriptorsDB::end() {
+ return st_descs.end();
+}
+
+std::vector<StDescriptors>::const_iterator StDescriptorsDB::begin() const {
+ return st_descs.cbegin();
+}
+
+std::vector<StDescriptors>::const_iterator StDescriptorsDB::end() const {
+ return st_descs.cend();
+}
--
GitLab