Merge branch 'develop' into refactor

Author: ErjieWu

source/module_io/write_elf.cpp

@@ -22,27 +22,34 @@ void write_elf(
     std::vector<std::vector<double>> elf(nspin, std::vector<double>(rho_basis->nrxx, 0.));
     // 1) calculate the kinetic energy density of vW KEDF
     std::vector<std::vector<double>> tau_vw(nspin, std::vector<double>(rho_basis->nrxx, 0.));
+    std::vector<double> phi(rho_basis->nrxx, 0.); // phi = sqrt(rho)
+
     for (int is = 0; is < nspin; ++is)
     {
-        std::vector<std::vector<double>> gradient_rho(3, std::vector<double>(rho_basis->nrxx, 0.));
-
-        std::vector<std::complex<double>> recip_rho(rho_basis->npw, 0.0);
-        std::vector<std::complex<double>> recip_gradient_rho(rho_basis->npw, 0.0);
-        rho_basis->real2recip(rho[is], recip_rho.data());
+        for (int ir = 0; ir < rho_basis->nrxx; ++ir)
+        {
+            phi[ir] = std::sqrt(std::abs(rho[is][ir]));
+        }
+        
+        std::vector<std::vector<double>> gradient_phi(3, std::vector<double>(rho_basis->nrxx, 0.));
+        std::vector<std::complex<double>> recip_phi(rho_basis->npw, 0.0);
+        std::vector<std::complex<double>> recip_gradient_phi(rho_basis->npw, 0.0);
+        
+        rho_basis->real2recip(phi.data(), recip_phi.data());
 
         std::complex<double> img(0.0, 1.0);
         for (int j = 0; j < 3; ++j)
         {
             for (int ip = 0; ip < rho_basis->npw; ++ip)
             {
-                recip_gradient_rho[ip] = img * rho_basis->gcar[ip][j] * recip_rho[ip] * rho_basis->tpiba;
+                recip_gradient_phi[ip] = img * rho_basis->gcar[ip][j] * recip_phi[ip] * rho_basis->tpiba;
             }
 
-            rho_basis->recip2real(recip_gradient_rho.data(), gradient_rho[j].data());
+            rho_basis->recip2real(recip_gradient_phi.data(), gradient_phi[j].data());
 
             for (int ir = 0; ir < rho_basis->nrxx; ++ir)
             {
-                tau_vw[is][ir] += gradient_rho[j][ir] * gradient_rho[j][ir] / (8. * rho[is][ir]) * 2.0; // convert Ha to Ry.
+                tau_vw[is][ir] += gradient_phi[j][ir] * gradient_phi[j][ir] / 2. * 2.; // convert Ha to Ry.
             }
         }
     }

source/version.h

@@ -1,3 +1,3 @@
 #ifndef VERSION
-#define VERSION "v3.9.0.3"
+#define VERSION "v3.9.0.4"
 #endif

tests/integrate/119_PW_out_elf/refELF.cube

@@ -1,7 +1,7 @@
-etotref -194.6234112615314
-etotperatomref -97.3117056308
+etotref -194.6234112652899
+etotperatomref -97.3117056326
 ComparePot1_pass 0
 pointgroupref T_d
 spacegroupref O_h
 nksibzref 1
-totaltimeref 0.25
+totaltimeref 0.32

tests/integrate/119_PW_out_elf/result.ref

@@ -1,7 +1,7 @@
-etotref -196.6254053459516
+etotref -196.6254053459514
 etotperatomref -98.3127026730
 ComparePot1_pass 0
 pointgroupref T_d
 spacegroupref O_h
 nksibzref 1
-totaltimeref 1.14
+totaltimeref 0.94

tests/integrate/219_NO_out_elf/refELF.cube

@@ -6,11 +6,12 @@
 # Only problem is the installation from github.com
 
 # Last Update in 2024-0119
+# Last Update in 2025-04-28 by Kai Luo
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 
-rapidjson_ver="1.1.0"
+rapidjson_ver="master" # latest version, instead of "1.1.0"  fixing issue of #5518
 rapidjson_sha256="bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e"
 source "${SCRIPT_DIR}"/common_vars.sh
 source "${SCRIPT_DIR}"/tool_kit.sh
@@ -31,8 +32,10 @@ case "$with_rapidjson" in
     pkg_install_dir="${INSTALLDIR}/$dirname"
     #pkg_install_dir="${HOME}/lib/rapidjson/${rapidjson_ver}"
     install_lock_file="$pkg_install_dir/install_successful"
-    url="https://github.com/Tencent/rapidjson/archive/refs/tags/v${rapidjson_ver}.tar.gz"
-    filename="rapidjson-${rapidjson_ver}.tar.gz"
+    #url="https://github.com/Tencent/rapidjson/archive/refs/tags/v${rapidjson_ver}.tar.gz" # commented by Kai Luo in 2025/04/28
+    url="https://codeload.github.com/Tencent/rapidjson/zip/refs/heads/master"
+    # filename="rapidjson-${rapidjson_ver}.tar.gz"
+    filename="rapidjson-${rapidjson_ver}.zip" # changed by Kai Luo in 2025/04/28
     if verify_checksums "${install_lock_file}"; then
         echo "$dirname is already installed, skipping it."
     else
@@ -41,14 +44,16 @@ case "$with_rapidjson" in
         else
         # download from github.com and checksum
             echo "===> Notice: This version of rapidjson is downloaded in GitHub Release, which will always be out-of-date version <==="
-            download_pkg_from_url "${rapidjson_sha256}" "${filename}" "${url}"
+            # download_pkg_from_url "${rapidjson_sha256}" "${filename}" "${url}"
+            wget  "${url}" -O  "${filename}"  --no-check-certificate # use wget directly instead of download_pkg_from_url
         fi
     if [ "${PACK_RUN}" = "__TRUE__" ]; then
       echo "--pack-run mode specified, skip installation"
     else
         echo "Installing from scratch into ${pkg_install_dir}"
         [ -d $dirname ] && rm -rf $dirname
-        tar -xzf $filename
+        # tar -xzf $filename
+        unzip -q $filename # downloaded file is a zip file, so use unzip instead of tar, use -q to suppress output
         mkdir -p "${pkg_install_dir}"
         cp -r $dirname/* "${pkg_install_dir}/"
         # for CMake to find rapidjson