Jastrow mu

configure.ac

@@ -98,6 +98,31 @@ case $CC in
         ;;
 esac
 
+# Check if `cp -r -n` works, otherwise use `cp -r`
+AC_CHECK_PROGS(CP_PROG, [cp])
+
+AC_MSG_CHECKING([for cp -r -n option])
+AC_RUN_IFELSE(
+    [AC_LANG_PROGRAM([
+#include <unistd.h>
+],[
+execl("/bin/sh", "sh", "-c", "mkdir tmpdir1 && \
+touch tmpdir1/test_file && \
+$CP_PROG -r -n tmpdir1 tmpdir2 && \
+exec ls tmpdir2/test_file", NULL);
+])],
+[ rm -rf tmpdir1 tmpdir2
+  CP_COMMAND="\"$CP_PROG\", \"-r\", \"-n\""
+  AC_MSG_RESULT([yes])],
+[ rm -rf tmpdir1 tmpdir2
+  CP_COMMAND="\"$CP_PROG\", \"-r\""
+  AC_MSG_RESULT([no])],
+[ rm -rf tmpdir1 tmpdir2
+  CP_COMMAND="\"$CP_PROG\", \"-r\""
+  AC_MSG_RESULT([no])]
+)
+AC_DEFINE_UNQUOTED([CP_COMMAND], [$CP_COMMAND], [Command used for trexio_cp])
+
 
 ## ---------
 ## Libraries
@@ -175,6 +200,9 @@ AC_TYPE_INT64_T
 AC_TYPE_SIZE_T
 AC_TYPE_UINT32_T
 AC_TYPE_UINT64_T
+AC_TYPE_PID_T
+AC_C_CONST
+AC_C_INLINE
 
 # Checks for library functions.
 # AC_FUNC_MALLOC

src/templates_front/templator_front.org

@@ -1590,7 +1590,7 @@ def _inquire(file_name: str) -> bool:
 
 ** File copy
 
-   ~trexio_cp~ copies a TREXIO file using =/bin/cp=.
+   ~trexio_cp~ copies a TREXIO file using =cp=.
 
    **Input parameters:**
      1) ~source_file_name~       - string containing the name of the source file
@@ -1650,24 +1650,14 @@ trexio_cp(const char* source, const char* dest)
 
   /* Call cp */
 
+#ifndef CP_COMMAND
+#define CP_COMMAND "cp", "-r"
+#endif
+
+
   pid_t pid = fork();
   if (pid == 0) {
-    switch (back_end_local) {
-    case TREXIO_TEXT:
-      execl("/bin/cp", "/bin/cp", "-r", "-n", source, dest, (char *)0);
-    case TREXIO_HDF5:
-#ifdef HAVE_HDF5
-      execl("/bin/cp", "/bin/cp", "-n", source, dest, (char *)0);
-#else
-      return TREXIO_FILE_ERROR;
-#endif
-/*
-    case TREXIO_JSON:
-      execl("/bin/cp", "/bin/cp", source, dest, (char *)0);
-,*/
-    default:
-      return TREXIO_FILE_ERROR;
-    }
+    execlp("cp", CP_COMMAND, source, dest, (char *)0);
   } else if (pid < 0) {
     return TREXIO_FILE_ERROR;
   } else {

trex.org

@@ -1132,12 +1132,7 @@ power = [
 
    The Jastrow factor is an $N$-electron function to which the CI
    expansion is multiplied: $\Psi = \Phi \times \exp(J)$,
-   where
 
-   \[
-   J(\mathbf{r},\mathbf{R}) = J_{\text{eN}}(\mathbf{r},\mathbf{R}) + J_{\text{ee}}(\mathbf{r}) + J_{\text{eeN}}(\mathbf{r},\mathbf{R})
-   \]
-
    In the following, we use the notations $r_{ij} = |\mathbf{r}_i - \mathbf{r}_j|$ and
    $R_{i\alpha} = |\mathbf{r}_i - \mathbf{R}_\alpha|$, where indices
    $i$ and $j$ correspond to electrons and $\alpha$ to nuclei.
@@ -1152,7 +1147,12 @@ power = [
 *** CHAMP
 
     The first form of Jastrow factor is the one used in
-    the [[https://trex-coe.eu/trex-quantum-chemistry-codes/champ][CHAMP]] program.
+    the [[https://trex-coe.eu/trex-quantum-chemistry-codes/champ][CHAMP]] program:
+
+   \[
+   J(\mathbf{r},\mathbf{R}) = J_{\text{eN}}(\mathbf{r},\mathbf{R}) + J_{\text{ee}}(\mathbf{r}) + J_{\text{eeN}}(\mathbf{r},\mathbf{R})
+   \]
+
 
    $J_{\text{eN}}$ contains electron-nucleus  terms:
 
@@ -1197,25 +1197,71 @@ power = [
    g_\alpha(r) = e^{-\kappa_\alpha\, r}.
    \]
 
-*** mu
+*** Mu
+
+   [[https://aip.scitation.org/doi/10.1063/5.0044683][Mu-Jastrow]] is based on a one-parameter correlation factor that has
+   been introduced in the context of transcorrelated methods.  This
+   correlation factor imposes the electron-electron cusp and it is
+   built such that the leading order in $1/r_{12}$ of the effective
+   two-electron potential reproduces the long-range interaction of the
+   range-separated density functional theory. Its analytical
+   expression reads 
+
+   \[
+   J(\mathbf{r}, \mathbf{R}) = J_{\text{eeN}}(\mathbf{r}, \mathbf{R}) + 
+                               J_{\text{eN}}(\mathbf{r}, \mathbf{R})
+   \].
+
+   The electron-electron cusp is incorporated in the three-body term.
+
+   \[
+   J_\text{eeN} (\mathbf{r}, \mathbf{R}) = 
+   \sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right) \,
+   \Pi_{\alpha=1}^{N_{\text{nucl}}} \, E_\alpha({R}_{i\alpha}) \, E_\alpha({R}_{j\alpha})
+   \]
+
+   $u$ is an electron-electron function is given by the symetric function
+
+   \[
+   u\left(\mu, r\right) = \frac{r}{2} \, \left[ 1 - \text{erf}(\mu\, r) \right] - \frac{1}{2 \, \mu \, \sqrt{\pi}} \exp \left[ -(\mu \, r)^2 \right].
+   \]
+
+   This electron-electron term is tuned by the parameter $\mu$ which
+   controls the depth and the range of the Coulomb hole between
+   electrons.
 
-    The "mu" Jastrow factor has only a single parameter $\mu$ for the
- [[https://doi.org/10.1063/5.0044683][electron-electron term]]: 
+   An envelope function has been introduced to cancel out the Jastrow
+   effects between two-electrons when they are both close to a nucleus
+   (to perform a frozen-core calculation). The envelope function is
+   given by
+
+   \[
+   E_\alpha(R) = 1 - \exp\left( - \gamma_{\alpha} \, R^2 \right).
+   \]
+
+   In particular, if the parameters $\gamma_\alpha$ tend to zero, the
+   Mu-Jastrow factor becomes a two-body Jastrow factor:
 
    \[
    J_{\text{ee}}(\mathbf{r}) = 
-   \sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} r_{ij}
-   \left( 1 - \text{erf}(\mu\, r_{ij})\right) - \frac{1}{\mu\sqrt{\pi}}
-   e^{-(\mu\,r_{ij})^2}
+   \sum_{i=1}^{N_\text{elec}} \sum_{j=1}^{i-1} \, u\left(\mu, r_{ij}\right) 
    \]
 
-#  It was then updated for frozen-core calculations by introducing a
-#  set of electron-electron-nucleus terms with one parameter per nucleus:
+   and for large $\gamma_\alpha$ it becomes zero.
+
+   To increase the flexibility of the Jastrow and improve the
+   electron density the following electron-nucleus term is added
+
+   \[
+   J_{\text{eN}}(\mathbf{r},\mathbf{R}) = \sum_{i=1}^{N_\text{elec}} \sum_{\alpha=1}^{N_\text{nucl}} \,
+   \left[ \exp\left( a_{\alpha} R_{i \alpha}^2 \right) - 1\right].
+   \]
 
-#  \[
-#  J_{\text{eeN}}(\mathbf{r}) =
-#  \]
 
+   The parameter $\mu$ is stored in the ~ee~ array, the parameters
+   $\gamma_\alpha$ are stored in the ~een~ array, and the parameters
+   $a_\alpha$ are stored in the ~en~ array.
+
 *** Table of values
 
    #+name: jastrow