Merge pull request #797 from brucefan1983/tools_readme

fix readme in tools

Author: brucefan1983

tools/cp2k2xyz/xyz2cp2k.sh

@@ -0,0 +1,80 @@
+#!/bin/bash
+
+#Read all frames of exyz and then calculate
+
+# CP2K environment setup
+source /home/chen/software/cp2k-2024.1/tools/toolchain/install/setup
+export PATH=$PATH:/home/chen/software/cp2k-2024.1/exe/local
+
+xyz_file="trj.xyz"
+template_inp="test.inp"
+
+# Set the number of cores
+num_cores=48  # You can change this value as needed
+
+# Debugging: Check the value of num_cores
+echo "Number of cores set to: $num_cores"
+
+frame_number=0  # Current frame counter
+
+while read -r line; do
+    if [[ $line =~ ^[0-9]+$ ]]; then
+        frame_number=$((frame_number + 1))
+        atom_count=$line
+        read -r frame_info
+        # Extract Lattice information and split into three triplets
+        lattice_values=$(echo $frame_info | grep -oP 'Lattice="\K[^"]+')
+        IFS=' ' read -r lattice_a1 lattice_a2 lattice_a3 lattice_b1 lattice_b2 lattice_b3 lattice_c1 lattice_c2 lattice_c3 <<< "$lattice_values"
+        
+        # Create a new input file
+        new_inp="frame${frame_number}.inp"
+        cp $template_inp $new_inp
+
+        # Modify the PROJECT line
+        sed -i "s/^  PROJECT.*/  PROJECT frame${frame_number}/" $new_inp
+
+        # Modify the CELL line, only replace between &SUBSYS and &COORD
+        sed -i "/&SUBSYS/,/&COORD/c\  &SUBSYS\n    &CELL\n      A    ${lattice_a1}    ${lattice_a2}    ${lattice_a3}\n      B    ${lattice_b1}    ${lattice_b2}    ${lattice_b3}\n      C    ${lattice_c1}    ${lattice_c2}    ${lattice_c3}\n      PERIODIC XYZ #Direction(s) of applied PBC (geometry aspect)\n    &END CELL\n    &COORD" $new_inp
+        
+        # Clear the COORD content
+        sed -i '/&COORD/,/&END COORD/c\    &COORD\n    &END COORD' $new_inp
+        
+        # Read atom coordinates and write to the new input file
+        for ((i=0; i<atom_count; i++)); do
+            read -r atom_line
+            # Extract element symbol and coordinate information
+            IFS=' ' read -r element x y z _ <<< "$atom_line"
+            sed -i "/&COORD/a\      $element $x $y $z" $new_inp
+        done
+    fi
+done < $xyz_file
+
+# Running CP2K for each input file
+for inp_file in frame*.inp; do
+    # Debugging: Print the command that will be run
+    echo "Running: mpirun -np $num_cores cp2k.popt $inp_file"
+    mpirun -np $num_cores cp2k.popt $inp_file | tee "${inp_file%.inp}.out"
+done
+
+# Merging output files
+merged_cell_file="merged.cell"
+merged_frc_file="merged-frc-1.xyz"
+merged_pos_file="merged-pos-1.xyz"
+
+# Remove old merged files if they exist
+rm -f $merged_cell_file $merged_frc_file $merged_pos_file
+
+# Concatenate each type of file
+for frame_number in $(seq 1 $frame_number); do
+    cat "frame${frame_number}-1.cell" >> $merged_cell_file
+    cat "frame${frame_number}-frc-1.xyz" >> $merged_frc_file
+    cat "frame${frame_number}-pos-1.xyz" >> $merged_pos_file
+done
+
+# Process merged.cell to retain only the first comment line
+awk '!/^#/ || !found { if (/^#/) found=1; print }' $merged_cell_file > temp && mv temp $merged_cell_file
+
+# Clean up individual frame files and input files
+for frame_number in $(seq 1 $frame_number); do
+    rm -f "frame${frame_number}.inp" "frame${frame_number}-1.cell" "frame${frame_number}-frc-1.xyz" "frame${frame_number}-pos-1.xyz" "frame${frame_number}.out" "frame${frame_number}-1.restart" "frame${frame_number}-1.ener"
+done

tools/for_coding/for_perioidc_table/a.out

@@ -9,7 +9,8 @@
 | -------------------- | ------------ | ------------------------------------------------------------ |
 | abacus2xyz           | Benrui Tang  | Get `train.xyz` from `ABACUS` outputs.                       |
 | add_groups           | Yuwen Zhang  | Generate grouping method(s) for `model.xyz`.                 |
-| castep2exyz          | Zerui Chen   | Get `train.xyz` from `CP2K` outputs.                         |
+| castep2exyz          | Yanzhou Wang | Get `train.xyz` from `CASTEP` outputs.                       |
+| cp2k2xyz             | Zherui Chen  | Get `train.xyz` from `CP2K` outputs or vice versa.           |
 | deep2nep             | Ke Xu        | Oudated?                                                     |
 | doc_3.3.1            | Zheyong Fan  | Documentation for some parts of GPUMD-v3.3.1.                |
 | dp2xyz               | Ke Xu        | Convert `DP` training data to xyz format.                    |
@@ -28,6 +29,6 @@
 | split_xyz            | Yong Wang    | Some functionalities for trainnig/test data.                 |
 | vasp2xyz             | Yanzhou Wang | Get `train.xyz` from `VASP` outputs.                         |
 | vim                  | Ke Xu        | Highlight GPUMD grammar in `vim`.                            |
-| xyz2gro              | Zerui Chen   | Convert `xyz` file to `gro` file.                            |
+| xyz2gro              | Zherui Chen  | Convert `xyz` file to `gro` file.                            |
 | [NepTrainKit](https://github.com/aboys-cb/NepTrainKit)           | Chengbing Chen| NEP data visualization interface program |