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Update binary format of dump custom

This commit is contained in:
Richard Berger 2020-08-13 14:45:22 -04:00
parent 71ec14087d
commit fbcc97586f
No known key found for this signature in database
GPG Key ID: A9E83994E0BA0CAB
4 changed files with 172 additions and 15 deletions

82
src/dump_custom.cpp
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@ -302,7 +302,7 @@ void DumpCustom::init_style()
strcpy(vformat[i],ptr);
}
vformat[i] = strcat(vformat[i]," ");
if (i+1 < size_one) vformat[i] = strcat(vformat[i]," ");
}
// setup boundary string
@ -381,8 +381,83 @@ void DumpCustom::write_header(bigint ndump)
/* ---------------------------------------------------------------------- */
void DumpCustom::format_magic_string_binary()
{
// use negative ntimestep as marker for new format
bigint fmtlen = strlen(MAGIC_STRING);
bigint marker = -fmtlen;
fwrite(&marker, sizeof(bigint), 1, fp);
fwrite(MAGIC_STRING, sizeof(char), fmtlen, fp);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::format_endian_binary()
{
int endian = ENDIAN;
fwrite(&endian, sizeof(int), 1, fp);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::format_revision_binary()
{
int revision = FORMAT_REVISION;
fwrite(&revision, sizeof(int), 1, fp);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::header_unit_style_binary()
{
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);
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::header_columns_binary()
{
int len = strlen(columns);
fwrite(&len, sizeof(int), 1, fp);
fwrite(columns, sizeof(char), len, fp);
}
/* ---------------------------------------------------------------------- */
void DumpCustom::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 DumpCustom::header_format_binary()
{
format_magic_string_binary();
format_endian_binary();
format_revision_binary();
}
/* ---------------------------------------------------------------------- */
void DumpCustom::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);
@ -394,6 +469,11 @@ void DumpCustom::header_binary(bigint ndump)
fwrite(&boxzlo,sizeof(double),1,fp);
fwrite(&boxzhi,sizeof(double),1,fp);
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);
else fwrite(&nprocs,sizeof(int),1,fp);
}

12
src/dump_custom.h
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@ -29,6 +29,10 @@ class DumpCustom : public Dump {
DumpCustom(class LAMMPS *, int, char **);
virtual ~DumpCustom();
const char * MAGIC_STRING = "DUMPCUSTOM";
const int FORMAT_REVISION = 0x0002;
const int ENDIAN = 0x0001;
protected:
int nevery; // dump frequency for output
int iregion; // -1 if no region, else which region
@ -107,6 +111,14 @@ class DumpCustom : public Dump {
int add_custom(char *, int);
virtual int modify_param(int, char **);
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();
void format_revision_binary();
typedef void (DumpCustom::*FnPtrHeader)(bigint);
FnPtrHeader header_choice; // ptr to write header functions
void header_binary(bigint);

1
unittest/formats/CMakeLists.txt
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@ -36,4 +36,5 @@ set_tests_properties(DumpCustom PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMM
if (BUILD_TOOLS)
set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$<TARGET_FILE:binary2txt>")
set_tests_properties(DumpCustom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$<TARGET_FILE:binary2txt>")
endif()

92
unittest/formats/test_dump_custom.cpp
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@ -24,46 +24,110 @@ char * BINARY2TXT_BINARY = nullptr;
class DumpCustomTest : public MeltTest {
};
TEST_F(DumpCustomTest, run0)
TEST_F(DumpCustomTest, run1)
{
auto dump_file = "dump_custom_run0.melt";
auto dump_file = "dump_custom_run1.melt";
if (!verbose) ::testing::internal::CaptureStdout();
command(fmt::format("dump id all custom 1 {} id type x y vx fx", dump_file));
command("run 0");
command("dump_modify id units yes");
command("run 1");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_STREQ(lines[4].c_str(), "ITEM: BOX BOUNDS pp pp pp");
ASSERT_EQ(utils::split_words(lines[5]).size(), 2);
ASSERT_STREQ(lines[8].c_str(), "ITEM: ATOMS id type x y vx fx");
ASSERT_EQ(utils::split_words(lines[9]).size(), 6);
ASSERT_EQ(lines.size(), 84);
ASSERT_STREQ(lines[6].c_str(), "ITEM: BOX BOUNDS pp pp pp");
ASSERT_EQ(utils::split_words(lines[7]).size(), 2);
ASSERT_STREQ(lines[10].c_str(), "ITEM: ATOMS id type x y vx fx");
ASSERT_EQ(utils::split_words(lines[11]).size(), 6);
delete_file(dump_file);
}
TEST_F(DumpCustomTest, triclinic_run0)
TEST_F(DumpCustomTest, binary_run1)
{
auto dump_file = "dump_custom_tri_run0.melt";
auto text_file = "dump_custom_text_run1.melt";
auto binary_file = "dump_custom_binary_run1.melt.bin";
auto converted_file = fmt::format("{}.txt", binary_file);
if(!BINARY2TXT_BINARY) GTEST_SKIP();
if (!verbose) ::testing::internal::CaptureStdout();
command(fmt::format("dump id0 all custom 1 {} id type x y vx fx", text_file));
command(fmt::format("dump id1 all custom 1 {} id type x y vx fx", binary_file));
command("dump_modify id0 units yes");
command("dump_modify id1 units yes");
command("run 1");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(binary_file);
if (!verbose) ::testing::internal::CaptureStdout();
std::string cmdline = fmt::format("{} {}", BINARY2TXT_BINARY, binary_file);
system(cmdline.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(binary_file);
delete_file(converted_file);
}
TEST_F(DumpCustomTest, triclinic_run1)
{
auto dump_file = "dump_custom_tri_run1.melt";
if (!verbose) ::testing::internal::CaptureStdout();
command("change_box all triclinic");
command(fmt::format("dump id all custom 1 {} id type x y vx fx", dump_file));
command("run 0");
command("dump_modify id units yes");
command("run 1");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_STREQ(lines[4].c_str(), "ITEM: BOX BOUNDS xy xz yz pp pp pp");
ASSERT_EQ(utils::split_words(lines[5]).size(), 3);
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(), 41);
ASSERT_EQ(lines.size(), 84);
delete_file(dump_file);
}
TEST_F(DumpCustomTest, binary_triclinic_run1)
{
auto text_file = "dump_custom_tri_text_run1.melt";
auto binary_file = "dump_custom_tri_binary_run1.melt.bin";
auto converted_file = fmt::format("{}.txt", binary_file);
if(!BINARY2TXT_BINARY) GTEST_SKIP();
if (!verbose) ::testing::internal::CaptureStdout();
command(fmt::format("dump id0 all custom 1 {} id type x y vx fx", text_file));
command(fmt::format("dump id1 all custom 1 {} id type x y vx fx", binary_file));
command("dump_modify id0 units yes");
command("dump_modify id1 units yes");
command("run 1");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(binary_file);
if (!verbose) ::testing::internal::CaptureStdout();
std::string cmdline = fmt::format("{} {}", BINARY2TXT_BINARY, binary_file);
system(cmdline.c_str());
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(binary_file);
delete_file(converted_file);
}
int main(int argc, char **argv)
{