add unit conversion to table pair style

src/pair_table.cpp

@@ -44,6 +44,7 @@ PairTable::PairTable(LAMMPS *lmp) : Pair(lmp)
 {
   ntables = 0;
   tables = NULL;
+  unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -360,7 +361,13 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
 {
   TableFileReader reader(lmp, file, "pair");
 
-  char * line = reader.find_section_start(keyword);
+  // transparently convert units for supported conversions
+
+  int unit_convert = reader.get_unit_convert();
+  double conversion_factor = utils::get_conversion_factor(utils::ENERGY,
+                                                          unit_convert);
+
+  char *line = reader.find_section_start(keyword);
 
   if (!line) {
     error->one(FLERR,"Did not find keyword in table file");
@@ -370,7 +377,7 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
   // allocate table arrays for file values
 
   line = reader.next_line();
-  param_extract(tb,line);
+  param_extract(tb, line);
   memory->create(tb->rfile,tb->ninput,"pair:rfile");
   memory->create(tb->efile,tb->ninput,"pair:efile");
   memory->create(tb->ffile,tb->ninput,"pair:ffile");
@@ -404,8 +411,8 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
       ValueTokenizer values(line);
       values.next_int();
       rfile = values.next_double();
-      tb->efile[i] = values.next_double();
+      tb->efile[i] = conversion_factor * values.next_double();
-      tb->ffile[i] = values.next_double();
+      tb->ffile[i] = conversion_factor * values.next_double();
     } catch (TokenizerException & e) {
       ++cerror;
     }
@@ -461,29 +468,26 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
     }
   }
 
-  if (ferror) {
+  if (ferror)
-    std::string str = fmt::format("{} of {} force values in table are inconsistent with -dE/dr.\n"
+    error->warning(FLERR,fmt::format("{} of {} force values in table are "
-                                  "  Should only be flagged at inflection points",ferror,tb->ninput);
+                                     "inconsistent with -dE/dr.\n  Should "
-    error->warning(FLERR,str.c_str());
+                                     "only be flagged at inflection points",
-  }
+                                     ferror,tb->ninput));
 
   // warn if re-computed distance values differ from file values
 
-  if (rerror) {
+  if (rerror)
-    char str[128];
+    error->warning(FLERR,fmt::format("{} of {} distance values in table with "
-    sprintf(str,"%d of %d distance values in table with relative error\n"
+                                     "relative error\n  over {} to "
-            "  over %g to re-computed values",rerror,tb->ninput,EPSILONR);
+                                     "re-computed values",
-    error->warning(FLERR,str);
+                                     rerror,tb->ninput,EPSILONR));
-  }
 
   // warn if data was read incompletely, e.g. columns were missing
 
-  if (cerror) {
+  if (cerror)
-    char str[128];
+    error->warning(FLERR,fmt::format("{} of {} lines in table were "
-    sprintf(str,"%d of %d lines in table were incomplete\n"
+                                     "incomplete\n  or could not be parsed "
-            "  or could not be parsed completely",cerror,tb->ninput);
+                                     "completely",cerror,tb->ninput));
-    error->warning(FLERR,str);
-  }
 }
 
 /* ----------------------------------------------------------------------

src/table_file_reader.cpp

@@ -27,17 +27,18 @@
 using namespace LAMMPS_NS;
 
 TableFileReader::TableFileReader(LAMMPS *lmp,
-                                         const std::string &filename,
+                                 const std::string &filename,
-                                         const std::string &type) :
+                                 const std::string &type,
-  PotentialFileReader(lmp, filename, type + " table")
+                                 const int auto_convert) :
+  PotentialFileReader(lmp, filename, type + " table", auto_convert)
 {
 }
 
 TableFileReader::~TableFileReader() {
 }
 
-char * TableFileReader::find_section_start(const std::string & keyword) {
+char *TableFileReader::find_section_start(const std::string & keyword) {
-  char * line = nullptr;
+  char *line = nullptr;
   while ((line = reader->next_line())) {
     ValueTokenizer values(line);
     std::string word = values.next_string();

src/table_file_reader.h

@@ -24,10 +24,11 @@ namespace LAMMPS_NS
 {
   class TableFileReader : public PotentialFileReader {
   public:
-    TableFileReader(class LAMMPS *lmp, const std::string &filename, const std::string & type);
+    TableFileReader(class LAMMPS *lmp, const std::string &filename,
+                    const std::string &type, const int auto_convert = 0);
     virtual ~TableFileReader();
 
-    char * find_section_start(const std::string & keyword);
+    char *find_section_start(const std::string &keyword);
   };
 
 } // namespace LAMMPS_NS

src/utils.cpp

@@ -687,7 +687,7 @@ double utils::get_conversion_factor(const int property, const int conversion)
     } else if (conversion == METAL2REAL) {
       return 23.060549;
     } else if (conversion == REAL2METAL) {
-      return 0.04336410204284381954;
+      return 1.0/23.060549;
     }
   }
   return 0.0;

unittest/formats/test_pair_unit_convert.cpp

@@ -140,6 +140,10 @@ TEST_F(PairUnitConvertTest, lj_cut)
     lmp->input->one("read_data test_pair_unit_convert.data");
     lmp->input->one("pair_style lj/cut 6.0");
     lmp->input->one("pair_coeff * * 0.01014286346782117 2.0");
+    remove("test.table.metal");
+    lmp->input->one("pair_write 1 1 1000 r 0.1 6.0 test.table.metal lj_1_1");
+    lmp->input->one("pair_write 1 2 1000 r 0.1 6.0 test.table.metal lj_1_2");
+    lmp->input->one("pair_write 2 2 1000 r 0.1 6.0 test.table.metal lj_2_2");
     lmp->input->one("run 0 post no");
     if (!verbose) ::testing::internal::GetCapturedStdout();
 
@@ -158,6 +162,10 @@ TEST_F(PairUnitConvertTest, lj_cut)
     lmp->input->one("read_data test_pair_unit_convert.data");
     lmp->input->one("pair_style lj/cut 6.0");
     lmp->input->one("pair_coeff * * 0.2339 2.0");
+    remove("test.table.real");
+    lmp->input->one("pair_write 1 1 1000 r 0.1 6.0 test.table.real lj_1_1");
+    lmp->input->one("pair_write 1 2 1000 r 0.1 6.0 test.table.real lj_1_2");
+    lmp->input->one("pair_write 2 2 1000 r 0.1 6.0 test.table.real lj_2_2");
     lmp->input->one("run 0 post no");
     if (!verbose) ::testing::internal::GetCapturedStdout();
 
@@ -216,6 +224,101 @@ TEST_F(PairUnitConvertTest, sw)
             EXPECT_NEAR(ev_convert * fold[i][j], f[i][j], fabs(f[i][j] * rel_error));
 }
 
+TEST_F(PairUnitConvertTest, table_metal2real)
+{
+    // check if the prerequisite pair style is available
+    if (!info->has_style("pair", "table")) GTEST_SKIP();
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    lmp->input->one("units metal");
+    lmp->input->one("read_data test_pair_unit_convert.data");
+    lmp->input->one("pair_style table linear 1000");
+    lmp->input->one("pair_coeff 1 1 test.table.metal lj_1_1");
+    lmp->input->one("pair_coeff 1 2 test.table.metal lj_1_2");
+    lmp->input->one("pair_coeff 2 2 test.table.metal lj_2_2");
+    lmp->input->one("run 0 post no");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    // copy pressure, energy, and force from first step
+    double pold;
+    lmp->output->thermo->evaluate_keyword("press", &pold);
+    double eold = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
+    double **f  = lmp->atom->f;
+    for (int i = 0; i < 4; ++i)
+        for (int j = 0; j < 3; ++j)
+            fold[i][j] = f[i][j];
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    lmp->input->one("clear");
+    lmp->input->one("units real");
+    lmp->input->one("read_data test_pair_unit_convert.data");
+    lmp->input->one("pair_style table linear 1000");
+    lmp->input->one("pair_coeff 1 1 test.table.metal lj_1_1");
+    lmp->input->one("pair_coeff 1 2 test.table.metal lj_1_2");
+    lmp->input->one("pair_coeff 2 2 test.table.metal lj_2_2");
+    lmp->input->one("run 0 post no");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    double pnew;
+    lmp->output->thermo->evaluate_keyword("press", &pnew);
+    EXPECT_NEAR(pold, p_convert * pnew, fabs(pnew * rel_error));
+    double enew = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
+    EXPECT_NEAR(ev_convert * eold, enew, fabs(enew * rel_error));
+
+    f = lmp->atom->f;
+    for (int i = 0; i < 4; ++i)
+        for (int j = 0; j < 3; ++j)
+            EXPECT_NEAR(ev_convert * fold[i][j], f[i][j], fabs(f[i][j] * rel_error));
+}
+
+TEST_F(PairUnitConvertTest, table_real2metal)
+{
+    // check if the prerequisite pair style is available
+    if (!info->has_style("pair", "table")) GTEST_SKIP();
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    lmp->input->one("units real");
+    lmp->input->one("read_data test_pair_unit_convert.data");
+    lmp->input->one("pair_style table linear 1000");
+    lmp->input->one("pair_coeff 1 1 test.table.real lj_1_1");
+    lmp->input->one("pair_coeff 1 2 test.table.real lj_1_2");
+    lmp->input->one("pair_coeff 2 2 test.table.real lj_2_2");
+    lmp->input->one("run 0 post no");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    // copy pressure, energy, and force from first step
+    double pold;
+    lmp->output->thermo->evaluate_keyword("press", &pold);
+    double eold = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
+    double **f  = lmp->atom->f;
+    for (int i = 0; i < 4; ++i)
+        for (int j = 0; j < 3; ++j)
+            fold[i][j] = f[i][j];
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    lmp->input->one("clear");
+    lmp->input->one("units metal");
+    lmp->input->one("read_data test_pair_unit_convert.data");
+    lmp->input->one("pair_style table linear 1000");
+    lmp->input->one("pair_coeff 1 1 test.table.real lj_1_1");
+    lmp->input->one("pair_coeff 1 2 test.table.real lj_1_2");
+    lmp->input->one("pair_coeff 2 2 test.table.real lj_2_2");
+    lmp->input->one("run 0 post no");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    double pnew;
+    lmp->output->thermo->evaluate_keyword("press", &pnew);
+    EXPECT_NEAR(pold, 1.0/p_convert * pnew, fabs(pnew * rel_error));
+    double enew = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
+    EXPECT_NEAR(1.0/ev_convert * eold, enew, fabs(enew * rel_error));
+
+    f = lmp->atom->f;
+    for (int i = 0; i < 4; ++i)
+        for (int j = 0; j < 3; ++j)
+            EXPECT_NEAR(1.0/ev_convert * fold[i][j], f[i][j],
+                        fabs(f[i][j] * rel_error));
+}
+
 TEST_F(PairUnitConvertTest, tersoff)
 {
     // check if the prerequisite pair style is available
@@ -539,5 +642,7 @@ int main(int argc, char **argv)
 
     int rv = RUN_ALL_TESTS();
     MPI_Finalize();
+    remove("test.table.metal");
+    remove("test.table.real");
     return rv;
 }