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Add UNITS information to dump atom binary format

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This commit is contained in:
Richard Berger
2020-08-13 10:49:03 -04:00
parent b27d63059c
commit 6d825dcb6b
3 changed files with 121 additions and 4 deletions
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28
src/dump_atom.cpp
View File

@ -204,6 +204,7 @@ void DumpAtom::header_format_binary()
void DumpAtom::header_binary(bigint ndump)
{
header_format_binary();
fwrite(&update->ntimestep,sizeof(bigint),1,fp);
fwrite(&ndump,sizeof(bigint),1,fp);
fwrite(&domain->triclinic,sizeof(int),1,fp);
@ -216,10 +217,22 @@ void DumpAtom::header_binary(bigint ndump)
fwrite(&boxzhi,sizeof(double),1,fp);
fwrite(&size_one,sizeof(int),1,fp);
int len = strlen(columns);
int len = 0;
if (unit_flag && !unit_count) {
++unit_count;
len = strlen(update->unit_style);
fwrite(&len, sizeof(int), 1, fp);
fwrite(update->unit_style, sizeof(char), len, fp);
} else {
fwrite(&len, sizeof(int), 1, fp);
}
len = strlen(columns);
fwrite(&len, sizeof(int), 1, fp);
fwrite(columns, sizeof(char), len, fp);
if (multiproc) fwrite(&nclusterprocs,sizeof(int),1,fp);
else fwrite(&nprocs,sizeof(int),1,fp);
}
@ -244,7 +257,18 @@ void DumpAtom::header_binary_triclinic(bigint ndump)
fwrite(&boxyz,sizeof(double),1,fp);
fwrite(&size_one,sizeof(int),1,fp);
int len = strlen(columns);
int len = 0;
if (unit_flag && !unit_count) {
++unit_count;
len = strlen(update->unit_style);
fwrite(&len, sizeof(int), 1, fp);
fwrite(update->unit_style, sizeof(char), len, fp);
} else {
fwrite(&len, sizeof(int), 1, fp);
}
len = strlen(columns);
fwrite(&len, sizeof(int), 1, fp);
fwrite(columns, sizeof(char), len, fp);

20
tools/binary2txt.cpp
View File

@ -93,7 +93,7 @@ int main(int narg, char **arg)
// detect newer format
char * magic_string = nullptr;
char * columns = nullptr;
char * unit_style = nullptr;
// loop over snapshots in file
@ -148,8 +148,20 @@ int main(int narg, char **arg)
fread(&size_one,sizeof(int),1,fp);
if (magic_string && revision > 0x0001) {
// newer format includes columns string
// newer format includes units and columns string
int len = 0;
fread(&len, sizeof(int), 1, fp);
if (len > 0) {
// has units
delete [] unit_style;
unit_style = new char[len+1];
fread(unit_style, sizeof(char), len, fp);
unit_style[len+1] = '\0';
fprintf(fptxt, "ITEM: UNITS\n");
fprintf(fptxt, "%s\n", unit_style);
}
fread(&len, sizeof(int), 1, fp);
delete [] columns;
columns = new char[len+1];
@ -229,6 +241,10 @@ int main(int narg, char **arg)
printf("\n");
delete [] columns;
delete [] magic_string;
delete [] unit_style;
columns = nullptr;
magic_string = nullptr;
unit_style = nullptr;
}
if (buf) delete [] buf;

77
unittest/formats/test_dump.cpp
View File

@ -270,6 +270,61 @@ TEST_F(DumpAtomTest, with_units_run1)
delete_file("dump_with_units_run1.melt");
}
TEST_F(DumpAtomTest, binary_with_units_run0)
{
if(!BINARY2TXT_BINARY) GTEST_SKIP();
if (!verbose) ::testing::internal::CaptureStdout();
command("dump id0 all atom 1 dump_text_with_units_run0.melt");
command("dump id1 all atom 1 dump_binary_with_units_run0.melt.bin");
command("dump_modify id0 scale no units yes");
command("dump_modify id1 scale no units yes");
command("run 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_text_with_units_run0.melt");
ASSERT_FILE_EXISTS("dump_binary_with_units_run0.melt.bin");
if (!verbose) ::testing::internal::CaptureStdout();
std::string cmdline = fmt::format("{} dump_binary_with_units_run0.melt.bin", BINARY2TXT_BINARY);
system(cmdline.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_binary_with_units_run0.melt.bin.txt");
ASSERT_FILE_EQUAL("dump_text_with_units_run0.melt", "dump_binary_with_units_run0.melt.bin.txt");
delete_file("dump_text_with_units_run0.melt");
delete_file("dump_binary_with_units_run0.melt.bin");
delete_file("dump_binary_with_units_run0.melt.bin.txt");
}
TEST_F(DumpAtomTest, binary_triclinic_with_units_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_units_run0.melt");
command("dump id1 all atom 1 dump_binary_tri_with_units_run0.melt.bin");
command("dump_modify id0 scale no units yes");
command("dump_modify id1 scale no units yes");
command("run 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_text_tri_with_units_run0.melt");
ASSERT_FILE_EXISTS("dump_binary_tri_with_units_run0.melt.bin");
if (!verbose) ::testing::internal::CaptureStdout();
std::string cmdline = fmt::format("{} dump_binary_tri_with_units_run0.melt.bin", BINARY2TXT_BINARY);
system(cmdline.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_binary_tri_with_units_run0.melt.bin.txt");
ASSERT_FILE_EQUAL("dump_text_tri_with_units_run0.melt", "dump_binary_tri_with_units_run0.melt.bin.txt");
delete_file("dump_text_tri_with_units_run0.melt");
delete_file("dump_binary_tri_with_units_run0.melt.bin");
delete_file("dump_binary_tri_with_units_run0.melt.bin.txt");
}
TEST_F(DumpAtomTest, no_buffer_with_scale_and_image_run0)
{
if (!verbose) ::testing::internal::CaptureStdout();
@ -307,6 +362,28 @@ TEST_F(DumpAtomTest, tricilinic_run0)
delete_file("dump_triclinic_run0.melt");
}
TEST_F(DumpAtomTest, tricilinic_with_units_run0)
{
if (!verbose) ::testing::internal::CaptureStdout();
command("change_box all triclinic");
command("dump id all atom 1 dump_triclinic_with_units_run0.melt");
command("dump_modify id units yes");
command("run 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS("dump_triclinic_with_units_run0.melt");
auto lines = read_lines("dump_triclinic_with_units_run0.melt");
ASSERT_STREQ(lines[0].c_str(), "ITEM: UNITS");
ASSERT_STREQ(lines[1].c_str(), "lj");
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_units_run0.melt");
}
TEST_F(DumpAtomTest, triclinic_with_image_run0)
{
if (!verbose) ::testing::internal::CaptureStdout();