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Add optional TIME to binary dump atom format

This commit is contained in:
Richard Berger 2020-08-13 11:48:29 -04:00
parent 6d80435b51
commit f9697bd9f5
No known key found for this signature in database
GPG Key ID: A9E83994E0BA0CAB
4 changed files with 122 additions and 1 deletions
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15
src/dump_atom.cpp
View File

@ -217,6 +217,19 @@ void DumpAtom::header_columns_binary()
/* ---------------------------------------------------------------------- */
void DumpAtom::header_time_binary()
{
char flag = time_flag ? 1 : 0;
fwrite(&flag, sizeof(char), 1, fp);
if (time_flag) {
double t = compute_time();
fwrite(&t, sizeof(double), 1, fp);
}
}
/* ---------------------------------------------------------------------- */
void DumpAtom::header_format_binary()
{
format_magic_string_binary();
@ -243,6 +256,7 @@ void DumpAtom::header_binary(bigint ndump)
fwrite(&size_one,sizeof(int),1,fp);
header_unit_style_binary();
header_time_binary();
header_columns_binary();
if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);
@ -271,6 +285,7 @@ void DumpAtom::header_binary_triclinic(bigint ndump)
fwrite(&size_one,sizeof(int),1,fp);
header_unit_style_binary();
header_time_binary();
header_columns_binary();
if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);

1
src/dump_atom.h
View File

@ -47,6 +47,7 @@ class DumpAtom : public Dump {
void header_format_binary();
void header_unit_style_binary();
void header_time_binary();
void header_columns_binary();
void format_magic_string_binary();
void format_endian_binary();

12
tools/binary2txt.cpp
View File

@ -148,7 +148,8 @@ int main(int narg, char **arg)
fread(&size_one,sizeof(int),1,fp);
if (magic_string && revision > 0x0001) {
// newer format includes units and columns string
// newer format includes units string, columns string
// and time
int len = 0;
fread(&len, sizeof(int), 1, fp);
@ -162,6 +163,15 @@ int main(int narg, char **arg)
fprintf(fptxt, "%s\n", unit_style);
}
char flag = 0;
fread(&flag, sizeof(char), 1, fp);
if (flag) {
double time;
fread(&time, sizeof(double), 1, fp);
fprintf(fptxt, "ITEM: TIME\n%.16g\n", time);
}
fread(&len, sizeof(int), 1, fp);
delete [] columns;
columns = new char[len+1];

95
unittest/formats/test_dump_atom.cpp
View File

@ -267,6 +267,25 @@ TEST_F(DumpAtomTest, with_units_run0)
delete_file("dump_with_units_run0.melt");
}
TEST_F(DumpAtomTest, with_time_run0)
{
if (!verbose) ::testing::internal::CaptureStdout();
command("dump id all atom 1 dump_with_time_run0.melt");
command("dump_modify id scale no time yes");
command("run 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_with_time_run0.melt");
auto lines = read_lines("dump_with_time_run0.melt");
ASSERT_EQ(lines.size(), 43);
ASSERT_STREQ(lines[0].c_str(), "ITEM: TIME");
ASSERT_STREQ(lines[10].c_str(), "ITEM: ATOMS id type x y z");
ASSERT_EQ(utils::split_words(lines[11]).size(), 5);
delete_file("dump_with_time_run0.melt");
}
TEST_F(DumpAtomTest, with_units_run1)
{
if (!verbose) ::testing::internal::CaptureStdout();
@ -342,6 +361,61 @@ TEST_F(DumpAtomTest, binary_triclinic_with_units_run0)
delete_file("dump_binary_tri_with_units_run0.melt.bin.txt");
}
TEST_F(DumpAtomTest, binary_with_time_run0)
{
if(!BINARY2TXT_BINARY) GTEST_SKIP();
if (!verbose) ::testing::internal::CaptureStdout();
command("dump id0 all atom 1 dump_text_with_time_run0.melt");
command("dump id1 all atom 1 dump_binary_with_time_run0.melt.bin");
command("dump_modify id0 scale no time yes");
command("dump_modify id1 scale no time yes");
command("run 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_text_with_time_run0.melt");
ASSERT_FILE_EXISTS("dump_binary_with_time_run0.melt.bin");
if (!verbose) ::testing::internal::CaptureStdout();
std::string cmdline = fmt::format("{} dump_binary_with_time_run0.melt.bin", BINARY2TXT_BINARY);
system(cmdline.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_binary_with_time_run0.melt.bin.txt");
ASSERT_FILE_EQUAL("dump_text_with_time_run0.melt", "dump_binary_with_time_run0.melt.bin.txt");
delete_file("dump_text_with_time_run0.melt");
delete_file("dump_binary_with_time_run0.melt.bin");
delete_file("dump_binary_with_time_run0.melt.bin.txt");
}
TEST_F(DumpAtomTest, binary_triclinic_with_time_run0)
{
if(!BINARY2TXT_BINARY) GTEST_SKIP();
if (!verbose) ::testing::internal::CaptureStdout();
command("change_box all triclinic");
command("dump id0 all atom 1 dump_text_tri_with_time_run0.melt");
command("dump id1 all atom 1 dump_binary_tri_with_time_run0.melt.bin");
command("dump_modify id0 scale no time yes");
command("dump_modify id1 scale no time yes");
command("run 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_text_tri_with_time_run0.melt");
ASSERT_FILE_EXISTS("dump_binary_tri_with_time_run0.melt.bin");
if (!verbose) ::testing::internal::CaptureStdout();
std::string cmdline = fmt::format("{} dump_binary_tri_with_time_run0.melt.bin", BINARY2TXT_BINARY);
system(cmdline.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_binary_tri_with_time_run0.melt.bin.txt");
ASSERT_FILE_EQUAL("dump_text_tri_with_time_run0.melt", "dump_binary_tri_with_time_run0.melt.bin.txt");
delete_file("dump_text_tri_with_time_run0.melt");
delete_file("dump_binary_tri_with_time_run0.melt.bin");
delete_file("dump_binary_tri_with_time_run0.melt.bin.txt");
}
TEST_F(DumpAtomTest, no_buffer_with_scale_and_image_run0)
{
if (!verbose) ::testing::internal::CaptureStdout();
@ -401,6 +475,27 @@ TEST_F(DumpAtomTest, tricilinic_with_units_run0)
delete_file("dump_triclinic_with_units_run0.melt");
}
TEST_F(DumpAtomTest, tricilinic_with_time_run0)
{
if (!verbose) ::testing::internal::CaptureStdout();
command("change_box all triclinic");
command("dump id all atom 1 dump_triclinic_with_time_run0.melt");
command("dump_modify id time yes");
command("run 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_triclinic_with_time_run0.melt");
auto lines = read_lines("dump_triclinic_with_time_run0.melt");
ASSERT_STREQ(lines[0].c_str(), "ITEM: TIME");
ASSERT_STREQ(lines[6].c_str(), "ITEM: BOX BOUNDS xy xz yz pp pp pp");
ASSERT_EQ(utils::split_words(lines[7]).size(), 3);
ASSERT_EQ(lines.size(), 43);
delete_file("dump_triclinic_with_time_run0.melt");
}
TEST_F(DumpAtomTest, triclinic_with_image_run0)
{
if (!verbose) ::testing::internal::CaptureStdout();