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Merge pull request brucefan1983#798 from zhyan0603/zhyan0603-GPUMD
clean up tools
2 parents c5ed706 + e16cf76 commit fa6c21f

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‎tools/cp2k2xyz/xyz2cp2k.sh‎

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@@ -9,6 +9,8 @@ export PATH=$PATH:/home/chen/software/cp2k-2024.1/exe/local
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xyz_file="trj.xyz"
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template_inp="test.inp"
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dos2unix ${xyz_file} ${template_inp}
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# Set the number of cores
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num_cores=48 # You can change this value as needed
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‎tools/exyz2pdb/exyz2pdb.tcl‎

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proc read_exyz {filename} {
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set file [open $filename "r"]
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set structures {}
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while {[gets $file line] >= 0} {
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set natoms [string trim $line]
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if {![gets $file line]} break
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set lattice {1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0}
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if {[regexp {Lattice="([^"]+)"} $line -> lattice_values]} {
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set lattice [split $lattice_values]
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}
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# Extract lattice vectors
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set a1 [lindex $lattice 0]; set a2 [lindex $lattice 1]; set a3 [lindex $lattice 2]
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set b1 [lindex $lattice 3]; set b2 [lindex $lattice 4]; set b3 [lindex $lattice 5]
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set c1 [lindex $lattice 6]; set c2 [lindex $lattice 7]; set c3 [lindex $lattice 8]
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# Calculate cell lengths
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set a [expr {sqrt($a1*$a1 + $a2*$a2 + $a3*$a3)}]
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set b [expr {sqrt($b1*$b1 + $b2*$b2 + $b3*$b3)}]
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set c [expr {sqrt($c1*$c1 + $c2*$c2 + $c3*$c3)}]
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# Calculate angles
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set alpha [expr {acos(($b1*$c1 + $b2*$c2 + $b3*$c3) / ($b*$c)) * 180 / 3.1415926535}]
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set beta [expr {acos(($a1*$c1 + $a2*$c2 + $a3*$c3) / ($a*$c)) * 180 / 3.1415926535}]
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set gamma [expr {acos(($a1*$b1 + $a2*$b2 + $a3*$b3) / ($a*$b)) * 180 / 3.1415926535}]
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set atoms {}
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for {set i 0} {$i < $natoms} {incr i} {
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gets $file line
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lappend atoms $line
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}
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lappend structures [list $a $b $c $alpha $beta $gamma $atoms]
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}
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close $file
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return $structures
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}
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proc write_pdb {structures output_filename} {
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set pdb_file [open $output_filename "w"]
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foreach structure $structures {
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lassign $structure a b c alpha beta gamma atoms
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puts $pdb_file [format "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1" $a $b $c $alpha $beta $gamma]
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set atom_index 1
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foreach atom $atoms {
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lassign [split $atom] element x y z
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puts $pdb_file [format "ATOM %5d %-4s MOL 1 %8.3f%8.3f%8.3f 1.00 0.00 %-2s" $atom_index $element $x $y $z $element]
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incr atom_index
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}
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puts $pdb_file "END"
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}
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close $pdb_file
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}
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# 使用示例
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set structures [read_exyz "2.xyz"]
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set pdb_filename "output_file.pdb"
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write_pdb $structures $pdb_filename
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# 加载生成的 PDB 文件并在 VMD 中显示
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mol new $pdb_filename

‎tools/gmx2exyz/gmx2exyz.py‎

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#Convert the trr trajectory of gmx to the exyz trajectory
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#write in the potential energy (eV) and atomic forces (eV/A)
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#Before use, run the gmx energy command to obtain the energy. xvg file that records potential energy
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#Author:Zherui Chen ([email protected])
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import MDAnalysis as mda
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u = mda.Universe('nvt.tpr', 'test.trr')
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sel = u.select_atoms('all', updating=False)
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# Load the energy file
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with open('energy.xvg', 'r') as f:
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for i in range(24):
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f.readline() # Skip the first 24 lines of comments
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energies = [float(line.split()[1]) / 96.48533212331 for line in f] # Convert from kJ/mol to eV
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with open('your_exyz_file.xyz', 'w') as f:
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for i, ts in enumerate(u.trajectory):
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f.write('{}\n'.format(sel.n_atoms))
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box = ts.dimensions[:3]
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f.write('energy={:.8f} config_type=gmx2xyz pbc="T T T" Lattice="{} 0.0 0.0 0.0 {} 0.0 0.0 0.0 {}" Properties=species:S:1:pos:R:3:force:R:3\n'.format(energies[i], box[0], box[1], box[2]))
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for atom in sel:
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# Get the force on the atom
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force = atom.force / 96.48533212331 # Convert from kJ/(mol*A) to eV/A
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# Write the atom element, position, and force to the output file
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f.write('{} {} {} {} {} {} {}\n'.format(atom.element, atom.position[0], atom.position[1], atom.position[2], force[0], force[1], force[2]))
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‎tools/readme.md‎

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* If you have questions on a tool, you can try to contact the creator.
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77

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| folder | creator | brief description |
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| -------------------- | ------------ | ------------------------------------------------------------ |
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| abacus2xyz | Benrui Tang | Get `train.xyz` from `ABACUS` outputs. |
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| add_groups | Yuwen Zhang | Generate grouping method(s) for `model.xyz`. |
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| castep2exyz | Yanzhou Wang | Get `train.xyz` from `CASTEP` outputs. |
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| cp2k2xyz | Zherui Chen | Get `train.xyz` from `CP2K` outputs or vice versa. |
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| deep2nep | Ke Xu | Oudated? |
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| doc_3.3.1 | Zheyong Fan | Documentation for some parts of GPUMD-v3.3.1. |
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| dp2xyz | Ke Xu | Convert `DP` training data to xyz format. |
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| for_coding | Zheyong Fan | Something useful for Zheyong Fan only. |
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| get_max_rmse_xyz | Who? | Identify sturctures with the largest force errors. |
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| gpumdkit | Zihan Yan | A shell toolkit for GPUMD |
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| md_tersoff | Zheyong Fan | Already in MD book; can be removed later. |
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| mtp2nep | Junjie Wang? | Outdated? |
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| mtp2xyz | Junjie Wang? | Convert `MTP` training data to xyz format. |
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| nep2xyz | Ke Xu | Outdated? |
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| pca_sampling | Penghua Ying | farthest-point sampling based on `calorine` |
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| perturbed2poscar | Who? | What? |
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| rdf_adf | Ke Xu | Calculate RDF and ADF using `OVITO`. |
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| runner2xyz | Ke Xu | Convert `RUNNER` training data to xyz format. |
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| shift_energy_to_zero | Nan Xu | Shift the average energy of each species to zero for a dataset. |
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| split_xyz | Yong Wang | Some functionalities for trainnig/test data. |
30-
| vasp2xyz | Yanzhou Wang | Get `train.xyz` from `VASP` outputs. |
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| vim | Ke Xu | Highlight GPUMD grammar in `vim`. |
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| xyz2gro | Zherui Chen | Convert `xyz` file to `gro` file. |
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| [NepTrainKit](https://github.com/aboys-cb/NepTrainKit) | Chengbing Chen| NEP data visualization interface program |
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| Folder | Creator | Email | Brief Description |
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| -------------------- | ------------ | ------------------------------------------------------------ | ------------------------------------------------------------ |
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| abacus2xyz | Benrui Tang | [email protected] | Get `train.xyz` from `ABACUS` outputs. |
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| add_groups | Yuwen Zhang | [email protected] | Generate grouping method(s) for `model.xyz`. |
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| castep2exyz | Yanzhou Wang | [email protected] | Get `train.xyz` from `CASTEP` outputs. |
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| cp2k2xyz | Zherui Chen | [email protected] | Get `train.xyz` from `CP2K` outputs or vice versa. |
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| deep2nep | Ke Xu | [email protected] | Oudated? |
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| doc_3.3.1 | Zheyong Fan | [email protected] | Documentation for some parts of GPUMD-v3.3.1. |
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| dp2xyz | Ke Xu | [email protected] | Convert `DP` training data to `xyz` format. |
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| exyz2pdb | Zherui Chem | [email protected] | Convert `exyz` to `pdb`. |
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| for_coding | Zheyong Fan | [email protected] | Something useful for Zheyong Fan only. |
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| get_max_rmse_xyz | Ke Xu | [email protected] | Identify structures with the largest errors. |
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| gmx2exyz | Zherui Chen | [email protected] | Convert the `trr` trajectory of `gmx` to the `exyz` trajectory. |
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| gpumdkit | Zihan Yan | [email protected] | A shell toolkit for GPUMD. |
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| md_tersoff | Zheyong Fan | [email protected] | Already in MD book; can be removed later. |
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| mtp2nep | Who? | | Outdated? |
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| mtp2xyz | Ke Xu | [email protected] | Convert `MTP` training data to xyz format. |
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| nep2xyz | Ke Xu | [email protected] | Outdated? |
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| pca_sampling | Penghua Ying | [email protected] | Farthest-point sampling based on `calorine`. |
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| perturbed2poscar | Who? | | What? |
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| rdf_adf | Ke Xu | [email protected] | Calculate RDF and ADF using `OVITO`. |
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| runner2xyz | Ke Xu | [email protected] | Convert `RUNNER` training data to `xyz` format. |
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| select_xyz_frames | Zherui Chen | [email protected] | Select frames from the `exyz` file. |
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| shift_energy_to_zero | Nan Xu | [email protected] | Shift the average energy of each species to zero for a dataset. |
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| split_xyz | Yong Wang | [email protected] | Some functionalities for training/test data. |
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| vasp2xyz | Yanzhou Wang | [email protected] | Get `train.xyz` from `VASP` outputs. |
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| vim | Ke Xu | [email protected] | Highlight GPUMD grammar in `vim`. |
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| xyz2gro | Who? | | Convert `xyz` file to `gro` file. |
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| [NepTrainKit](https://github.com/aboys-cb/NepTrainKit) | Chengbing Chen| [email protected] | NEP data visualization interface program. |

‎tools/select_xyz_frames/select_xyz_frames.py‎

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#Select frames from the exyz trajectory file.
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#When an atom in a frame experiences a force greater than the force_threshold in any direction, the frame is removed. eV/A
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#When the total energy difference between adjacent frames is less than energy_threshold, only one frame is retained. eV
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#When the RMSD difference between adjacent frames is less than rmsd_threshold, only one frame is retained. A^2
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#If set to 'not', do not select based on this condition.
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#Author:Zherui Chen ([email protected])
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import numpy as np
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def parse_xyz_file(filename):
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with open(filename, 'r') as file:
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lines = file.readlines()
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frames = []
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i = 0
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while i < len(lines):
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num_atoms = int(lines[i].strip())
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frame_info = lines[i + 1].strip()
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energy_str = frame_info.split('energy=')[1].split()[0]
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energy = float(energy_str)
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lattice_str = frame_info.split('Lattice="')[1].split('"')[0]
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lattice = np.array(list(map(float, lattice_str.split()))).reshape(3, 3)
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atoms = lines[i + 2:i + 2 + num_atoms]
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frames.append((num_atoms, frame_info, energy, lattice, atoms))
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i += 2 + num_atoms
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return frames
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def force_exceeds_threshold(atom_line, threshold):
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if threshold == "not":
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return False
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forces = list(map(float, atom_line.split()[4:7]))
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return any(abs(force) > threshold for force in forces)
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def calculate_rmsd(frame1_atoms, frame2_atoms, lattice):
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num_atoms = len(frame1_atoms)
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rmsd_sum = 0.0
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for atom1, atom2 in zip(frame1_atoms, frame2_atoms):
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pos1 = np.array(list(map(float, atom1.split()[1:4])))
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pos2 = np.array(list(map(float, atom2.split()[1:4])))
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# Calculate the minimum image distance
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diff = pos2 - pos1
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diff -= np.round(diff @ np.linalg.inv(lattice)) @ lattice
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rmsd_sum += np.dot(diff, diff)
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return np.sqrt(rmsd_sum / num_atoms)
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def filter_frames(frames, force_threshold, energy_threshold, rmsd_threshold):
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filtered_frames = []
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if frames:
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filtered_frames.append(frames[0])
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for j in range(1, len(frames)):
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prev_frame = filtered_frames[-1]
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current_frame = frames[j]
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num_atoms, frame_info, energy, lattice, atoms = current_frame
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if force_threshold != "not" and any(force_exceeds_threshold(atom, force_threshold) for atom in atoms):
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continue
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if energy_threshold != "not":
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prev_energy = prev_frame[2]
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if abs(energy - prev_energy) < energy_threshold:
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continue
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if rmsd_threshold != "not":
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prev_atoms = prev_frame[4]
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rmsd = calculate_rmsd(prev_atoms, atoms, lattice)
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if rmsd < rmsd_threshold:
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continue
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filtered_frames.append(current_frame)
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return filtered_frames
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def write_xyz_file(frames, output_filename):
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with open(output_filename, 'w') as file:
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for num_atoms, frame_info, energy, lattice, atoms in frames:
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file.write(f"{num_atoms}\n")
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file.write(f"{frame_info}\n")
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for atom in atoms:
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file.write(f"{atom.strip()}\n")
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force_threshold = 20.0
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energy_threshold = "not"
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rmsd_threshold = "not"
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input_filename = 'coal-nep.xyz'
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output_filename = 'output.xyz'
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frames = parse_xyz_file(input_filename)
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filtered_frames = filter_frames(frames, force_threshold, energy_threshold, rmsd_threshold)
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write_xyz_file(filtered_frames, output_filename)
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print(f"Filtered frames written to {output_filename}")

‎tools/vasp2xyz/outcar2xyz/multipleFrames-outcars2nep-exyz.sh‎

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@@ -33,6 +33,8 @@ total_outcar=$(find -L "$read_dire" -name "OUTCAR" | wc -l)
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converged_files=()
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non_converged_files=()
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echo "Checking the convergence of OUTCARs ..."
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for file in $(find "$read_dire" -name "OUTCAR"); do
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NSW=$(grep "number of steps for IOM" "$file" | awk '{print $3}')
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‎tools/vasp2xyz/outcar2xyz/singleFrame-outcars2nep-exyz.sh‎

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if [[ $viri_logi -eq 1 ]]
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then
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viri=$(grep -A 20 "FORCE on cell =-STRESS" $i | grep "Total " | tail -n 1 | awk '{print $2,$5,$7,$5,$3,$6,$7,$6,$4}')
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echo "Config_type=$configuration Weight=1.0 Lattice=\"$latt\" Energy=$ener Virial=\"$viri\" Properties=species:S:1:pos:R:3:forces:R:3" >> $writ_dire/$writ_file
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echo "Config_type=$configuration Weight=1.0 Lattice=\"$latt\" Energy=$ener Virial=\"$viri\" pbc=\"T T T\" Properties=species:S:1:pos:R:3:forces:R:3" >> $writ_dire/$writ_file
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else
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echo "Config_type=$configuration Weight=1.0 Lattice=\"$latt\" Energy=$ener Properties=species:S:1:pos:R:3:forces:R:3" >> $writ_dire/$writ_file
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echo "Config_type=$configuration Weight=1.0 Lattice=\"$latt\" Energy=$ener pbc=\"T T T\" Properties=species:S:1:pos:R:3:forces:R:3" >> $writ_dire/$writ_file
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fi
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ion_numb_arra=($(grep "ions per type" $i | tail -n 1 | awk -F"=" '{print $2}'))
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ion_symb_arra=($(grep "POTCAR:" $i | awk '{print $3}' | awk -F"_" '{print $1}' | awk '!seen[$0]++'))

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