Merge pull request #3507 from hammondkd/thermo_mod_range

Support thermo_modify format column index ranges

doc/src/Modify_style.rst

@@ -359,6 +359,12 @@ you are uncertain, please ask.
 
 - I/O is done via the C-style stdio library and **not** iostreams.
 
+- Do not use so-called "alternative tokens" like ``and``, ``or``,
+  ``not`` and similar, but rather use the corresponding operators
+  ``&&``, ``||``, and ``!``.  The alternative tokens are not available
+  by default on all compilers, and also we want to maintain a consistent
+  programming style.
+
 - Output to the screen and the logfile should be using the corresponding
   FILE pointers and only be done on MPI rank 0.  Use the :cpp:func:`utils::logmesg`
   convenience function where possible.

doc/src/thermo_modify.rst

@@ -28,6 +28,7 @@ Syntax
        *format* values = *line* string, *int* string, *float* string, ID string, or *none*
          string = C-style format string
          ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* an integer range such as 2*6 (negative values are not allowed)
               *or* a thermo keyword or reference to compute, fix, property or variable.
        *temp* value = compute ID that calculates a temperature
        *press* value = compute ID that calculates a pressure
@@ -65,10 +66,10 @@ atom can be "lost" if it moves across a non-periodic simulation box
 :doc:`boundary <boundary>` or if it moves more than a box length outside
 the simulation domain (or more than a processor sub-domain length)
 before reneighboring occurs.  The latter case is typically due to bad
-dynamics, e.g. too large a timestep or huge forces and velocities.  If
+dynamics (e.g., too large a time step and/or huge forces and velocities).  If
 the value is *ignore*, LAMMPS does not check for lost atoms.  If the
 value is *error* or *warn*, LAMMPS checks and either issues an error or
-warning.  The code will exit with an error and continue with a warning.
+warning.  The simulation will exit with an error and continue with a warning.
 A warning will only be issued once, the first time an atom is lost.
 This can be a useful debugging option.
 
@@ -89,10 +90,10 @@ that should be investigated, but LAMMPS cannot determine for
 certain whether they are an indication of an error.
 
 Some warning messages are printed during a run (or immediately before)
-each time a specific MPI rank encounters the issue, e.g. bonds that are
-stretched too far or dihedrals in extreme configurations. These number
+each time a specific MPI rank encounters the issue (e.g., bonds that are
+stretched too far or dihedrals in extreme configurations). These number
 of these can quickly blow up the size of the log file and screen output.
-Thus a limit of 100 warning messages is applied by default.  The warning
+Thus, a limit of 100 warning messages is applied by default.  The warning
 count is applied to the entire input unless reset with a ``thermo_modify
 warn reset`` command.  If there are more warnings than the limit, LAMMPS
 will print one final warning that it will not print any additional
@@ -160,8 +161,8 @@ for a column or field of thermodynamic output.  The setting for *ID
 string* replaces the default text with the provided string.  *ID* can be
 a positive integer when it represents the column number counting from
 the left, a negative integer when it represents the column number from
-the right (i.e. -1 is the last column/keyword), or a thermo keyword (or
-compute, fix, property, or variable reference) and then it replaces the
+the right (i.e., :math:`-1` is the last column/keyword), or a thermo keyword
+(or compute, fix, property, or variable reference) and then it replaces the
 string for that specific thermo keyword.
 
 The *colname* keyword can be used multiple times. If multiple *colname*
@@ -171,19 +172,22 @@ to their default values.
 
 The *format* keyword can be used to change the default numeric format of
 any of quantities the :doc:`thermo_style <thermo_style>` command
-outputs.  All the specified format strings are C-style formats, e.g. as
-used by the C/C++ printf() command.  The *line* keyword takes a single
+outputs.  All the specified format strings are C-style formats (i.e., as
+used by the C/C++ printf() command).  The *line* keyword takes a single
 argument which is the format string for the entire line of thermo
-output, with N fields, which you must enclose in quotes if it is more
+output, with :math:`N` fields, which you must enclose in quotes if it is more
 than one field.  The *int* and *float* keywords take a single format
 argument and are applied to all integer or floating-point quantities
 output.  The setting for *ID string* also takes a single format argument
-which is used for the indexed value in each line.  The interpretation is
-the same as for *colname*, i.e. a positive integer is the n-th value
+that is used for the indexed value in each line.  The interpretation is
+the same as for *colname* (i.e., a positive integer is the n-th value
 corresponding to the n-th thermo keyword, a negative integer is counting
-backwards, and a string matches the entry with the thermo keyword.,
-e.g. the fifth column is output in high precision for "format 5 %20.15g"
-and the pair energy for "format epair %20.15g".
+backwards, and a string matches the entry with the thermo keyword).
+For example, the fifth column is output in high precision for
+"format 5 %20.15g", and the pair energy for "format epair %20.15g".
+The *ID* field can be a range, such as "3\*6", "*", "2*", or "\*3";
+in such cases, all fields in the range (inclusive) are set to the specified
+format string. Ranges containing negative numbers are not supported.
 
 The *format* keyword can be used multiple times.  The precedence is
 that for each value in a line of output, the *ID* format (if specified)
@@ -201,8 +205,8 @@ settings, reverting all values to their default format.
    to the corresponding 8-byte form when it is applied to those
    keywords.  However, when specifying the *line* option or *format ID
    string* option for *step* and *natoms*, you should specify a format
-   string appropriate for an 8-byte signed integer, e.g. one with "%ld"
-   or "%lld" depending on the platform.
+   string appropriate for an 8-byte signed integer (i.e., one with "%ld"
+   or "%lld", depending on the platform).
 
 The *temp* keyword is used to determine how thermodynamic temperature is
 calculated, which is used by all thermo quantities that require a

src/thermo.cpp

@@ -678,6 +678,19 @@ void Thermo::modify_params(int narg, char **arg)
             format_int_user.replace(found, 1, std::string(BIGINT_FORMAT).substr(1));
       } else if (strcmp(arg[iarg + 1], "float") == 0) {
         format_float_user = arg[iarg + 2];
+      } else if (utils::strmatch(arg[iarg + 1], "^\\d*\\*\\d*$")) {
+        // handles cases such as 2*6; currently doesn't allow negatives
+        int nlo, nhi;
+        utils::bounds(FLERR, arg[iarg + 1], 1, nfield_initial, nlo, nhi, error);
+        int icol = -1;
+        for (int i = nlo - 1; i < nhi; i++) {
+          if (i < 0) icol = nfield_initial + i + 1; // doesn't happen currently
+          else icol = i;
+          if (icol < 0 || (icol >= nfield_initial))
+            error->all(FLERR, "Invalid thermo_modify format argument: {}",
+              arg[iarg + 1]);
+          format_column_user[icol] = arg[iarg + 2];
+        }
       } else {
         int icol = -1;
         if (utils::is_integer(arg[iarg + 1])) {

unittest/utils/test_utils.cpp

@@ -631,6 +631,18 @@ TEST(Utils, strmatch_whitespace_nonwhitespace)
     ASSERT_TRUE(utils::strmatch(" 5.0  angles\n", "^\\s*\\S+\\s+\\S+\\s"));
 }
 
+TEST(Utils, strmatch_range)
+{
+    ASSERT_TRUE(utils::strmatch("*11", "^\\d*\\*\\d*$"));
+    ASSERT_TRUE(utils::strmatch("2*11", "^\\d*\\*\\d*$"));
+    ASSERT_TRUE(utils::strmatch("5*", "^\\d*\\*\\d*$"));
+    ASSERT_TRUE(utils::strmatch("*", "^\\d*\\*\\d*$"));
+    ASSERT_FALSE(utils::strmatch("x5*", "^\\d*\\*\\d*$"));
+    ASSERT_FALSE(utils::strmatch("x*", "^\\d*\\*\\d*$"));
+    ASSERT_FALSE(utils::strmatch("*a", "^\\d*\\*\\d*$"));
+    ASSERT_FALSE(utils::strmatch("1*2d", "^\\d*\\*\\d*$"));
+}
+
 TEST(Utils, strfind_beg)
 {
     ASSERT_THAT(utils::strfind("rigid/small/omp", "^rigid"), StrEq("rigid"));