Migrate changes to dump custom/gz and add tests

src/COMPRESS/dump_custom_gz.cpp

@@ -15,8 +15,10 @@
 #include "domain.h"
 #include "error.h"
 #include "update.h"
+#include "force.h"
 
 #include <cstring>
+#include <fmt/format.h>
 
 using namespace LAMMPS_NS;
 
@@ -25,6 +27,8 @@ DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) :
 {
   gzFp = NULL;
 
+  compression_level = Z_BEST_COMPRESSION;
+
   if (!compressed)
     error->all(FLERR,"Dump custom/gz only writes compressed files");
 }
@@ -91,12 +95,15 @@ void DumpCustomGZ::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
+    std::string mode;
     if (append_flag) {
-      gzFp = gzopen(filecurrent,"ab9");
+      mode = fmt::format("ab{}", compression_level);
     } else {
-      gzFp = gzopen(filecurrent,"wb9");
+      mode = fmt::format("wb{}", compression_level);
     }
 
+    gzFp = gzopen(filecurrent, mode.c_str());
+
     if (gzFp == NULL) error->one(FLERR,"Cannot open dump file");
   } else gzFp = NULL;
 
@@ -120,14 +127,14 @@ void DumpCustomGZ::write_header(bigint ndump)
     gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
     if (domain->triclinic == 0) {
       gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
-      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);
+      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
-      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);
+      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
-      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);
+      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
     } else {
       gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
-      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);
+      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
-      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);
+      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
-      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);
+      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz);
     }
     gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
   }
@@ -156,3 +163,20 @@ void DumpCustomGZ::write()
   }
 }
 
+/* ---------------------------------------------------------------------- */
+
+int DumpCustomGZ::modify_param(int narg, char **arg)
+{
+  int consumed = DumpCustom::modify_param(narg, arg);
+  if(consumed == 0) {
+    if (strcmp(arg[0],"compression_level") == 0) {
+      if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
+      int min_level = Z_DEFAULT_COMPRESSION;
+      int max_level = Z_BEST_COMPRESSION;
+      if (compression_level < 0 || compression_level > max_level)
+        error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level));
+      return 2;
+    }
+  }
+  return consumed;
+}

src/COMPRESS/dump_custom_gz.h

@@ -31,12 +31,15 @@ class DumpCustomGZ : public DumpCustom {
   virtual ~DumpCustomGZ();
 
  protected:
+  int compression_level;
   gzFile gzFp;  // file pointer for the compressed output stream
 
   virtual void openfile();
   virtual void write_header(bigint);
   virtual void write_data(int, double *);
   virtual void write();
+
+  virtual int modify_param(int, char **);
 };
 
 }

unittest/formats/CMakeLists.txt

@@ -31,12 +31,19 @@ set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS
 
 if (PKG_COMPRESS)
     find_program(GZIP_BINARY NAMES gzip REQUIRED)
+
     add_executable(test_dump_atom_gz test_dump_atom_gz.cpp)
     target_link_libraries(test_dump_atom_gz PRIVATE lammps GTest::GMock GTest::GTest)
     add_test(NAME DumpAtomGZ COMMAND test_dump_atom_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
     set_tests_properties(DumpAtomGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}")
 
+    add_executable(test_dump_custom_gz test_dump_custom_gz.cpp)
+    target_link_libraries(test_dump_custom_gz PRIVATE lammps GTest::GMock GTest::GTest)
+    add_test(NAME DumpCustomGZ COMMAND test_dump_custom_gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+    set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
+    set_tests_properties(DumpCustomGZ PROPERTIES ENVIRONMENT "GZIP_BINARY=${GZIP_BINARY}")
+
     find_program(ZSTD_BINARY NAMES zstd)
 
     if (ZSTD_BINARY)

unittest/formats/test_dump_custom_gz.cpp

@@ -0,0 +1,140 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "gtest/gtest.h"
+#include "gmock/gmock.h"
+#include "fmt/format.h"
+#include "utils.h"
+#include "../testing/core.h"
+#include "../testing/systems/melt.h"
+#include "../testing/utils.h"
+
+using ::testing::Eq;
+
+char * GZIP_BINARY = nullptr;
+
+class DumpCustomGZTest : public MeltTest {
+    std::string dump_style = "custom";
+public:
+    void enable_triclinic() {
+        if (!verbose) ::testing::internal::CaptureStdout();
+        command("change_box all triclinic");
+        if (!verbose) ::testing::internal::GetCapturedStdout();
+    }
+
+    void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options, int ntimesteps) {
+        if (!verbose) ::testing::internal::CaptureStdout();
+        command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, fields));
+
+        if (!dump_modify_options.empty()) {
+            command(fmt::format("dump_modify id {}", dump_modify_options));
+        }
+
+        command(fmt::format("run {}", ntimesteps));
+        if (!verbose) ::testing::internal::GetCapturedStdout();
+    }
+
+    void generate_text_and_compressed_dump(std::string text_file, std::string compressed_file, std::string compression_style,
+                                           std::string fields, std::string dump_modify_options, int ntimesteps) {
+        if (!verbose) ::testing::internal::CaptureStdout();
+        command(fmt::format("dump id0 all {} 1 {} {}", dump_style, text_file, fields));
+        command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_file, fields));
+
+        if (!dump_modify_options.empty()) {
+            command(fmt::format("dump_modify id0 {}", dump_modify_options));
+            command(fmt::format("dump_modify id1 {}", dump_modify_options));
+        }
+
+        command(fmt::format("run {}", ntimesteps));
+        if (!verbose) ::testing::internal::GetCapturedStdout();
+    }
+
+    std::string convert_compressed_to_text(std::string compressed_file) {
+        if (!verbose) ::testing::internal::CaptureStdout();
+        std::string converted_file = compressed_file.substr(0, compressed_file.find_last_of('.'));
+        std::string cmdline = fmt::format("{} -d -c {} > {}", GZIP_BINARY, compressed_file, converted_file);
+        system(cmdline.c_str());
+        if (!verbose) ::testing::internal::GetCapturedStdout();
+        return converted_file;
+    }
+};
+
+TEST_F(DumpCustomGZTest, compressed_run1)
+{
+    if(!GZIP_BINARY) GTEST_SKIP();
+
+    auto text_file = "dump_custom_text_run1.melt";
+    auto compressed_file = "dump_custom_compressed_run1.melt.gz";
+    auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz";
+
+    generate_text_and_compressed_dump(text_file, compressed_file, "custom/gz", fields, "units yes", 1);
+
+    ASSERT_FILE_EXISTS(text_file);
+    ASSERT_FILE_EXISTS(compressed_file);
+
+    auto converted_file = convert_compressed_to_text(compressed_file);
+
+    ASSERT_FILE_EXISTS(converted_file);
+    ASSERT_FILE_EQUAL(text_file, converted_file);
+    delete_file(text_file);
+    delete_file(compressed_file);
+    delete_file(converted_file);
+}
+
+TEST_F(DumpCustomGZTest, compressed_triclinic_run1)
+{
+    if(!GZIP_BINARY) GTEST_SKIP();
+
+    auto text_file = "dump_custom_tri_text_run1.melt";
+    auto compressed_file = "dump_custom_tri_compressed_run1.melt.gz";
+    auto fields = "id type proc x y z xs ys zs xsu ysu zsu vx vy vz fx fy fz";
+    
+    enable_triclinic();
+
+    generate_text_and_compressed_dump(text_file, compressed_file, "custom/gz", fields, "units yes", 1);
+
+    ASSERT_FILE_EXISTS(text_file);
+    ASSERT_FILE_EXISTS(compressed_file);
+
+    auto converted_file = convert_compressed_to_text(compressed_file);
+
+    ASSERT_FILE_EXISTS(converted_file);
+    ASSERT_FILE_EQUAL(text_file, converted_file);
+    delete_file(text_file);
+    delete_file(compressed_file);
+    delete_file(converted_file);
+}
+
+int main(int argc, char **argv)
+{
+    MPI_Init(&argc, &argv);
+    ::testing::InitGoogleMock(&argc, argv);
+
+    // handle arguments passed via environment variable
+    if (const char *var = getenv("TEST_ARGS")) {
+        std::vector<std::string> env = utils::split_words(var);
+        for (auto arg : env) {
+            if (arg == "-v") {
+                verbose = true;
+            }
+        }
+    }
+
+    GZIP_BINARY = getenv("GZIP_BINARY");
+
+    if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
+
+    int rv = RUN_ALL_TESTS();
+    MPI_Finalize();
+    return rv;
+}