Latex formulas update

CHANGELOG.md

@@ -6,6 +6,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## Unreleased
+
+### Added
+
+- Added `ClexulatorWriter.generated_files` attribute, holding a list of the files generated when writing a Clexulator
+- Added generation of latex formulas during the Clexulator writing process
+- Added `casm.bset.cluster_functions.MakeVariableName` for variable naming
+
+### Changed
+
+- Updated `ClexulatorWriter.write` to write a "variables.json" file for each Clexulator (including local Clexulator) which contains the variables used by the jinja2 templates as well as information like basis function formulas generated during the write process
+- Changed the name used for occupation variables. The name "\\phi" is the base, but the number and meaning of the indices can vary depending on the site basis functions. An "occ_site_functions_info" dict in the "variables.json" file contains the string value used as a template ("occ_var_name") and a description of the variable including its indices, if any ("occ_var_desc").
+
+
 ## [2.0a1] - 2024-08-15
 
 This release creates the casm-bset CASM cluster expansion basis set construction module. This includes:

casm/bset/clexwriter/_cpp_str.py

@@ -5,6 +5,7 @@
 from casm.bset.misc import (
     almost_equal,
     factor_by_mode,
+    irrational_to_tex_string,
 )
 from casm.bset.polynomial_functions import (
     PolynomialFunction,
@@ -50,6 +51,7 @@ def occ_func_cpp_str(
     var: Variable,
     prim_neighbor_list: PrimNeighborList,
     occupant_index_argname: str,
+    mode: str = "cpp",
 ) -> str:
     """Return a C++ expression to evaluate an occupation site basis variable
 
@@ -62,6 +64,8 @@ def occ_func_cpp_str(
         The primitive neighbor list, used to find the sublattice index
     occupant_index_argname: str
         The occupant index argument name. Usually "occ_i" or "occ_f".
+    mode: str = "cpp"
+        The mode for the output. Options are "cpp" and "latex".
 
     Returns
     -------
@@ -82,12 +86,21 @@ def occ_func_cpp_str(
     i = var.neighborhood_site_index % len(nlist_sublat_indices)
     b = nlist_sublat_indices[i]
     m = var.site_basis_function_index
-    return f"m_occ_func_{b}_{m}[{occupant_index_argname}]"
+    n = var.neighborhood_site_index
+    if mode == "cpp":
+        return f"m_occ_func_{b}_{m}[{occupant_index_argname}]"
+    elif mode == "latex":
+        return f"{var.name}({occupant_index_argname}_{{{n}}})"
+        # return f"\\phi_{{{b},{m}}}({occupant_index_argname}_{{{n}}})"
+    else:
+        raise ValueError(f"Invalid mode: {mode}")
 
 
 def variable_cpp_str(
     var: Variable,
     prim_neighbor_list: PrimNeighborList,
+    mode: str = "cpp",
+    label_site_using: str = "neighborhood_site_index",
 ) -> str:
     """Return a C++ expression to access an evaluated variable
 
@@ -97,6 +110,11 @@ def variable_cpp_str(
         The variable to be accessed.
     prim_neighbor_list: PrimNeighborList
         The PrimNeighborList used when constructing the functions.
+    mode: str = "cpp"
+        The mode for the output. Options are "cpp" and "latex".
+    label_site_using = "neighborhood_site_index"
+        The label to use for the site index in the output. Options are
+        "neighborhood_site_index" and "cluster_site_index".
 
     Returns
     -------
@@ -112,16 +130,43 @@ def variable_cpp_str(
         b = nlist_sublat_indices[i]
         m = var.site_basis_function_index
         n = var.neighborhood_site_index
-        return f"occ_func_{b}_{m}({n})"
+        cl = var.cluster_site_index
+        if mode == "cpp":
+            return f"occ_func_{b}_{m}({n})"
+        elif mode == "latex":
+            if label_site_using == "neighborhood_site_index":
+                return f"{var.name}(\\vec{{r}}_{{{n}}})"
+            elif label_site_using == "cluster_site_index":
+                return f"{var.name}(\\vec{{r}}_{{{cl}}})"
+            else:
+                raise ValueError(f"Invalid label_site_using: {label_site_using}")
+        else:
+            raise ValueError(f"Invalid mode: {mode}")
     elif var.neighborhood_site_index is not None:
         # local continuous DoF
         c = var.component_index
         n = var.neighborhood_site_index
-        return f"{var.key}_var_{c}<Scalar>({n})"
+        cl = var.cluster_site_index
+        if mode == "cpp":
+            return f"{var.key}_var_{c}<Scalar>({n})"
+        elif mode == "latex":
+            if label_site_using == "neighborhood_site_index":
+                return f"{var.name}(\\vec{{r}}_{{{n}}})"
+            elif label_site_using == "cluster_site_index":
+                return f"{var.name}(\\vec{{r}}_{{{cl}}})"
+            else:
+                raise ValueError(f"Invalid label_site_using: {label_site_using}")
+        else:
+            raise ValueError(f"Invalid mode: {mode}")
     else:
         # global continuous DoF
         c = var.component_index
-        return f"{var.key}_var<Scalar>({c})"
+        if mode == "cpp":
+            return f"{var.key}_var<Scalar>({c})"
+        elif mode == "latex":
+            return f"{var.name}"
+        else:
+            raise ValueError(f"Invalid mode: {mode}")
 
 
 def monomial_cpp_str(
@@ -130,6 +175,8 @@ def monomial_cpp_str(
     monomial_exponents: np.ndarray,
     prim_neighbor_list: PrimNeighborList,
     cpp_fmt: CppFormatProperties,
+    mode: str = "cpp",
+    label_site_using: str = "neighborhood_site_index",
 ) -> str:
     """Return a C++ expression to evaluate a monomial
 
@@ -143,6 +190,11 @@ def monomial_cpp_str(
         The PrimNeighborList used when constructing the functions.
     cpp_fmt: CppFormatProperties
         C++ string formatting properties.
+    mode: str = "cpp"
+        The mode for the output. Options are "cpp" and "latex".
+    label_site_using = "neighborhood_site_index"
+        The label to use for the site index in the output. Options are
+        "neighborhood_site_index" and "cluster_site_index".
 
     Returns
     -------
@@ -161,16 +213,31 @@ def monomial_cpp_str(
     for i_var, x in enumerate(monomial_exponents):
         if x == 0:
             continue
-        v = variable_cpp_str(variables[i_var], prim_neighbor_list)
+        v = variable_cpp_str(
+            variables[i_var],
+            prim_neighbor_list,
+            mode=mode,
+            label_site_using=label_site_using,
+        )
         if use_mul:
-            op = "*"
+            if mode == "cpp":
+                op = "*"
+            elif mode == "latex":
+                op = " "
+            else:
+                raise ValueError(f"Invalid mode: {mode}")
         else:
             op = ""
             use_mul = True
         if x == 1:
             cpp_str += f"{op}{v}"
         else:
-            cpp_str += f"{op}pow({v},{x})"
+            if mode == "cpp":
+                cpp_str += f"{op}pow({v},{x})"
+            elif mode == "latex":
+                cpp_str += f"{op}{v}^{{{x}}}"
+            else:
+                raise ValueError(f"Invalid mode: {mode}")
     return cpp_str
 
 
@@ -179,6 +246,8 @@ def polynomial_sum_cpp_str(
     normalization: float,
     prim_neighbor_list: PrimNeighborList,
     cpp_fmt: CppFormatProperties,
+    mode: str = "cpp",
+    label_site_using: str = "neighborhood_site_index",
 ) -> str:
     """Return a C++ expression to evaluate a polynomial expression
 
@@ -194,6 +263,11 @@ def polynomial_sum_cpp_str(
         The PrimNeighborList used when constructing the functions.
     cpp_fmt: CppFormatProperties
         C++ string formatting properties.
+    mode: str = "cpp"
+        The mode for the output. Options are "cpp" and "latex".
+    label_site_using = "neighborhood_site_index"
+        The label to use for the site index in the output. Options are
+        "neighborhood_site_index" and "cluster_site_index".
 
     Returns
     -------
@@ -215,7 +289,15 @@ def polynomial_sum_cpp_str(
 
     cpp_str = ""
     if not is_one(common_prefix, atol=cpp_fmt.coeff_atol):
-        cpp_str += f"{common_prefix:{cpp_fmt.coeff_fmt_spec}} * "
+        if mode == "cpp":
+            cpp_str += f"{common_prefix:{cpp_fmt.coeff_fmt_spec}} * "
+        elif mode == "latex":
+            limit = len(functions[0].variables) ** 2
+            max_pow = 2
+            common_prefix_tex = irrational_to_tex_string(
+                common_prefix, limit=limit, max_pow=max_pow, abs_tol=1e-5
+            )
+            cpp_str += f"{common_prefix_tex} "
     if len(functions) > 1:
         cpp_str += "(\n"
 
@@ -230,7 +312,8 @@ def polynomial_sum_cpp_str(
             orbit_use_plus = True
         if not is_one(factored_prefixes[i_func], atol=cpp_fmt.coeff_atol):
             cpp_str += f"{factored_prefixes[i_func]:{cpp_fmt.coeff_fmt_spec}} * "
-        cpp_str += "("
+        if len(function.monomial_exponents) > 1:
+            cpp_str += "("
         cluster_use_plus = False
         for i_monomial, _monomial_exponents in enumerate(function.monomial_exponents):
             if cluster_use_plus:
@@ -244,8 +327,11 @@ def polynomial_sum_cpp_str(
                 monomial_exponents=_monomial_exponents,
                 prim_neighbor_list=prim_neighbor_list,
                 cpp_fmt=cpp_fmt,
+                mode=mode,
+                label_site_using=label_site_using,
             )
-        cpp_str += ")"
+        if len(function.monomial_exponents) > 1:
+            cpp_str += ")"
         if len(functions) > 1:
             cpp_str += "\n"
 
@@ -261,6 +347,8 @@ def orbit_bfunc_cpp_str(
     orbit_size: int,
     prim_neighbor_list: PrimNeighborList,
     cpp_fmt: CppFormatProperties,
+    mode: str = "cpp",
+    label_site_using: str = "neighborhood_site_index",
 ) -> str:
     """Return a C++ expression to evaluate a single orbit basis function
 
@@ -276,6 +364,11 @@ def orbit_bfunc_cpp_str(
         The PrimNeighborList used when constructing the functions.
     cpp_fmt: CppFormatProperties
         C++ string formatting properties.
+    mode: str = "cpp"
+        The mode for the output. Options are "cpp" and "latex".
+    label_site_using = "neighborhood_site_index"
+        The label to use for the site index in the output. Options are
+        "neighborhood_site_index" and "cluster_site_index".
 
     Returns
     -------
@@ -290,6 +383,8 @@ def orbit_bfunc_cpp_str(
         normalization=float(orbit_size),
         prim_neighbor_list=prim_neighbor_list,
         cpp_fmt=cpp_fmt,
+        mode=mode,
+        label_site_using=label_site_using,
     )
 
 
@@ -298,6 +393,8 @@ def site_bfunc_cpp_str(
     orbit_size: int,
     prim_neighbor_list: PrimNeighborList,
     cpp_fmt: CppFormatProperties,
+    mode: str = "cpp",
+    label_site_using: str = "neighborhood_site_index",
 ) -> Optional[str]:
     """Return a C++ expression to evaluate a single point correlation function
 
@@ -313,6 +410,8 @@ def site_bfunc_cpp_str(
         The PrimNeighborList used when constructing the functions.
     cpp_fmt: CppFormatProperties
         C++ string formatting properties.
+    mode: str = "cpp"
+        The mode for the output. Options are "cpp" and "latex".
 
     Returns
     -------
@@ -328,6 +427,8 @@ def site_bfunc_cpp_str(
         normalization=float(orbit_size),
         prim_neighbor_list=prim_neighbor_list,
         cpp_fmt=cpp_fmt,
+        mode=mode,
+        label_site_using=label_site_using,
     )
 
 
@@ -337,6 +438,8 @@ def occ_delta_site_bfunc_cpp_str(
     orbit_size: int,
     prim_neighbor_list: PrimNeighborList,
     cpp_fmt: CppFormatProperties,
+    mode: str = "cpp",
+    label_site_using: str = "neighborhood_site_index",
 ) -> Optional[str]:
     """Return a C++ expression to evaluate the change in a single point correlation \
     function due to a change in occupation
@@ -355,6 +458,8 @@ def occ_delta_site_bfunc_cpp_str(
         The PrimNeighborList used when constructing the functions.
     cpp_fmt: CppFormatProperties
         C++ string formatting properties.
+    mode: str = "cpp"
+        The mode for the output. Options are "cpp" and "latex".
 
     Returns
     -------
@@ -407,16 +512,27 @@ def find_occ_site_var(monomial: PolynomialFunction):
     indent = "  "
     cpp_str = ""
     use_plus = False
+    if mode == "cpp":
+        occupant_index_argname_final = "occ_f"
+        occupant_index_argname_init = "occ_i"
+    elif mode == "latex":
+        occupant_index_argname_final = "\\vec{r}^{\\ f}"
+        occupant_index_argname_init = "\\vec{r}^{\\ i}"
+    else:
+        raise ValueError(f"Invalid mode: {mode}")
+
     for var, factored_point_functions in occ_delta_functions.items():
         site_var_final = occ_func_cpp_str(
             var=var,
             prim_neighbor_list=prim_neighbor_list,
-            occupant_index_argname="occ_f",
+            occupant_index_argname=occupant_index_argname_final,
+            mode=mode,
         )
         site_var_init = occ_func_cpp_str(
             var=var,
             prim_neighbor_list=prim_neighbor_list,
-            occupant_index_argname="occ_i",
+            occupant_index_argname=occupant_index_argname_init,
+            mode=mode,
         )
         if use_plus:
             cpp_str += "\n\n" + indent * 1 + " + "
@@ -428,5 +544,7 @@ def find_occ_site_var(monomial: PolynomialFunction):
             normalization=float(orbit_size),
             prim_neighbor_list=prim_neighbor_list,
             cpp_fmt=cpp_fmt,
+            mode=mode,
+            label_site_using=label_site_using,
         )
     return cpp_str