Closed WeJear closed 9 months ago
I tried another one and another error occurred In addition, the water-dp directory contains md.log, .enrg, frc-1.xyz, *pos-1.xyz files
import dpdata file_label = "water" data = dpdata.LabeledSystem('{}-dp'.format(file_label), fmt="cp2kdata/md") print(data)
The following is the error:
--- You are parsing data using package Cp2kData --- Traceback (most recent call last): File "/home/xwj/materials/water/water-deepmd/water-dp.py", line 12, in
data = dpdata.LabeledSystem('{}-dp'.format(file_label), fmt="cp2kdata/md") File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 183, in init self.from_fmt( File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 220, in from_fmt return self.from_fmt_obj(load_format(fmt), file_name, kwargs) File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 1113, in from_fmt_obj data = fmtobj.from_labeled_system(file_name, kwargs) File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/dpdata_plugin.py", line 73, in from_labeled_system cp2kmd = Cp2kOutput(output_file=cp2k_output_name, run_type="MD", path_prefix=path_prefix) File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/output.py", line 84, in init parse_run_type() File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/output.py", line 311, in parse_md self.md_info = parse_md_info(self.filename) File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/block_parser/header_info.py", line 109, in parse_md_info md_info = regrep( File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/monty/re.py", line 36, in regrep gen = reverse_readfile(filename) if reverse else zopen(filename, "rt") File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/monty/io.py", line 37, in zopen name, ext = os.path.splitext(filename) File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/posixpath.py", line 118, in splitext p = os.fspath(p) TypeError: expected str, bytes or os.PathLike object, not NoneType
Hope you can help me find out what's wrong。Thanks
input file is not used in parsing. I found the error may arise from you log file. Need the log file to debug
which version of cp2k are you using?
no need, you can run your case with 2-3 steps md. and upload whole files to github
which version of cp2k are you using?
The version I am using is 9.1. If possible, I can send the log file to your email.
no need, you can run your case with 2-3 steps md. and upload whole files to github
Okay, I'll try it.
no need, you can run your case with 2-3 steps md. and upload whole files to github
Okay, I'll try it.
I'm very sorry, I am only responsible for training potential functions, I am not good at the molecular dynamics of cp2k. It's too late today, I can only ask others tomorrow. So I won’t take up your time tonight. Thank you for replying to my question. I will chat with you in detail tomorrow.
no need, you can run your case with 2-3 steps md. and upload whole files to github
Okay, I'll try it.
I'm very sorry, I am only responsible for training potential functions, I am not good at the molecular dynamics of cp2k. It's too late today, I can only ask others tomorrow. So I won’t take up your time tonight. Thank you for replying to my question. I will chat with you in detail tomorrow.
I am in other time zone. Won't reply so quickly.
no need, you can run your case with 2-3 steps md. and upload whole files to github
Okay, I'll try it.
I'm very sorry, I am only responsible for training potential functions, I am not good at the molecular dynamics of cp2k. It's too late today, I can only ask others tomorrow. So I won’t take up your time tonight. Thank you for replying to my question. I will chat with you in detail tomorrow.
I am in other time zone. Won't reply so quickly.
It's okay, you can help me in your free time. Thank you again.
no need, you can run your case with 2-3 steps md. and upload whole files to github
I've got the files. I hope you can help me take a look at it. Thank you. water-dp.zip
Great, I found the simulation is driven by xTB. But cp2kdata was design for parsing DFT data for now. I will label this as enhancement and update ASAP.
Great, I found the simulation is driven by xTB. But cp2kdata was design for parsing DFT data for now. I will label this as enhancement and update ASAP.
Okay, thank you for your hard work
Try install the cp2kdata from devel branch. It can be used to parse NPT_I of xTB for now. commit: 1fae663e2fded526f07e313cde444e6dea16eb54
import dpdata
cp2kmd_dir = "./test"
cp2kmd_output_name = "58-water.log"
dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md")
print(dp)
--- You are parsing data using package Cp2kData ---
Parsing Energies from ./test/water-300K-1.ener
Parsing Structures from ./test/water-300K-pos-1.xyz
Parsing Froces from ./test/water-300K-nvt.force-frc-1.xyz
Parsing Stress from the CP2K output/log file: ./test/58-water.log
Parsing Cells Information from ./test/58-water.log
Atom names are fake chemical symbols as you set in cp2k input.
--- You are parsing data using package Cp2kData ---
Data Summary
Labeled System
-------------------
Frame Numbers : 1026
Atom Numbers : 174
Including Virials : No
Element List :
-------------------
H O
116 58
Still the cp2k files are too large for me. I will put your case in cp2kdata testsuit to ensure the code is robust for future development. Could you compute or ask your colleague for helping compute the md with only 2-3 steps. Just modify the
&MOTION
&MD
ENSEMBLE NPT_I
STEPS 5000 -> 2 or 3 is ok
STEPS
from 5000 to 2 or 3. And upload the whole folder. Thank you in advance
Okay, I will do this as you said tomorrow, thank you for your hard work
Try install the cp2kdata from devel branch. It can be used to parse NPT_I of xTB for now. commit: 1fae663
import dpdata cp2kmd_dir = "./test" cp2kmd_output_name = "58-water.log" dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md") print(dp)
--- You are parsing data using package Cp2kData --- Parsing Energies from ./test/water-300K-1.ener Parsing Structures from ./test/water-300K-pos-1.xyz Parsing Froces from ./test/water-300K-nvt.force-frc-1.xyz Parsing Stress from the CP2K output/log file: ./test/58-water.log Parsing Cells Information from ./test/58-water.log Atom names are fake chemical symbols as you set in cp2k input. --- You are parsing data using package Cp2kData --- Data Summary Labeled System ------------------- Frame Numbers : 1026 Atom Numbers : 174 Including Virials : No Element List : ------------------- H O 116 58
Still the cp2k files are too large for me. I will put your case in cp2kdata testsuit to ensure the code is robust for future development. Could you compute or ask your colleague for helping compute the md with only 2-3 steps. Just modify the
&MOTION &MD ENSEMBLE NPT_I STEPS 5000 -> 2 or 3 is ok
STEPS
from 5000 to 2 or 3. And upload the whole folder. Thank you in advance
Okay, I will do this as you said tomorrow, thank you for your hard work
Try install the cp2kdata from devel branch. It can be used to parse NPT_I of xTB for now. commit: 1fae663
import dpdata cp2kmd_dir = "./test" cp2kmd_output_name = "58-water.log" dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md") print(dp)
--- You are parsing data using package Cp2kData --- Parsing Energies from ./test/water-300K-1.ener Parsing Structures from ./test/water-300K-pos-1.xyz Parsing Froces from ./test/water-300K-nvt.force-frc-1.xyz Parsing Stress from the CP2K output/log file: ./test/58-water.log Parsing Cells Information from ./test/58-water.log Atom names are fake chemical symbols as you set in cp2k input. --- You are parsing data using package Cp2kData --- Data Summary Labeled System ------------------- Frame Numbers : 1026 Atom Numbers : 174 Including Virials : No Element List : ------------------- H O 116 58
Still the cp2k files are too large for me. I will put your case in cp2kdata testsuit to ensure the code is robust for future development. Could you compute or ask your colleague for helping compute the md with only 2-3 steps. Just modify the
&MOTION &MD ENSEMBLE NPT_I STEPS 5000 -> 2 or 3 is ok
STEPS
from 5000 to 2 or 3. And upload the whole folder. Thank you in advanceTry install the cp2kdata from devel branch. It can be used to parse NPT_I of xTB for now. commit: 1fae663
import dpdata cp2kmd_dir = "./test" cp2kmd_output_name = "58-water.log" dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md") print(dp)
--- You are parsing data using package Cp2kData --- Parsing Energies from ./test/water-300K-1.ener Parsing Structures from ./test/water-300K-pos-1.xyz Parsing Froces from ./test/water-300K-nvt.force-frc-1.xyz Parsing Stress from the CP2K output/log file: ./test/58-water.log Parsing Cells Information from ./test/58-water.log Atom names are fake chemical symbols as you set in cp2k input. --- You are parsing data using package Cp2kData --- Data Summary Labeled System ------------------- Frame Numbers : 1026 Atom Numbers : 174 Including Virials : No Element List : ------------------- H O 116 58
Still the cp2k files are too large for me. I will put your case in cp2kdata testsuit to ensure the code is robust for future development. Could you compute or ask your colleague for helping compute the md with only 2-3 steps. Just modify the
&MOTION &MD ENSEMBLE NPT_I STEPS 5000 -> 2 or 3 is ok
STEPS
from 5000 to 2 or 3. And upload the whole folder. Thank you in advance
I tested the code. In the case of a small amount of data, it could run well. But when my step is at 20,000, the code runs stuck for a long time, and I can't make sure whether it is running correctly.
import dpdata
data = dpdata.LabeledSystem('water-dp', cp2k_output_name = 'md.log', fmt="cp2kdata/md")
print(data)
(deepmd) xwj@ERNIC:~/materials/water/water-deepmd$ python water-dp.py
--- You are parsing data using package Cp2kData ---
Parsing Energies from water-dp/water-300K-1.ener
Parsing Structures from water-dp/water-300K-pos-1.xyz
It is expected. since the cell information is stored in the huge output file, the code has to go through the file, which takes time.
It is expected. since the cell information is stored in the huge output file, the code has to go through the file, which takes time.
ok , i will try longer time
Try install the cp2kdata from devel branch. It can be used to parse NPT_I of xTB for now. commit: 1fae663
import dpdata cp2kmd_dir = "./test" cp2kmd_output_name = "58-water.log" dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md") print(dp)
--- You are parsing data using package Cp2kData --- Parsing Energies from ./test/water-300K-1.ener Parsing Structures from ./test/water-300K-pos-1.xyz Parsing Froces from ./test/water-300K-nvt.force-frc-1.xyz Parsing Stress from the CP2K output/log file: ./test/58-water.log Parsing Cells Information from ./test/58-water.log Atom names are fake chemical symbols as you set in cp2k input. --- You are parsing data using package Cp2kData --- Data Summary Labeled System ------------------- Frame Numbers : 1026 Atom Numbers : 174 Including Virials : No Element List : ------------------- H O 116 58
Still the cp2k files are too large for me. I will put your case in cp2kdata testsuit to ensure the code is robust for future development. Could you compute or ask your colleague for helping compute the md with only 2-3 steps. Just modify the
&MOTION &MD ENSEMBLE NPT_I STEPS 5000 -> 2 or 3 is ok
STEPS
from 5000 to 2 or 3. And upload the whole folder. Thank you in advanceTry install the cp2kdata from devel branch. It can be used to parse NPT_I of xTB for now. commit: 1fae663
import dpdata cp2kmd_dir = "./test" cp2kmd_output_name = "58-water.log" dp = dpdata.LabeledSystem(cp2kmd_dir, cp2k_output_name=cp2kmd_output_name, fmt="cp2kdata/md") print(dp)
--- You are parsing data using package Cp2kData --- Parsing Energies from ./test/water-300K-1.ener Parsing Structures from ./test/water-300K-pos-1.xyz Parsing Froces from ./test/water-300K-nvt.force-frc-1.xyz Parsing Stress from the CP2K output/log file: ./test/58-water.log Parsing Cells Information from ./test/58-water.log Atom names are fake chemical symbols as you set in cp2k input. --- You are parsing data using package Cp2kData --- Data Summary Labeled System ------------------- Frame Numbers : 1026 Atom Numbers : 174 Including Virials : No Element List : ------------------- H O 116 58
Still the cp2k files are too large for me. I will put your case in cp2kdata testsuit to ensure the code is robust for future development. Could you compute or ask your colleague for helping compute the md with only 2-3 steps. Just modify the
&MOTION &MD ENSEMBLE NPT_I STEPS 5000 -> 2 or 3 is ok
STEPS
from 5000 to 2 or 3. And upload the whole folder. Thank you in advance
I've got the files and I hope this helps. water-dp.zip
Great. It helps.
When I was using the dpdata package to convert the output of cp2k aimd, some errors occurred. Hopefully someone can help me figure out what the problem is.
The following is the error: --- You are parsing data using package Cp2kData --- Traceback (most recent call last): File "/home/xwj/materials/water/water-deepmd/water-dp.py", line 10, in
data = dpdata.LabeledSystem('./{}-dp'.format(file_label), cp2k_output_name = 'md.log', fmt="cp2kdata/md")
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 183, in init
self.from_fmt(
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 220, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, kwargs)
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 1113, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, kwargs)
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/dpdata_plugin.py", line 73, in from_labeled_system
cp2kmd = Cp2kOutput(output_file=cp2k_output_name, run_type="MD", path_prefix=path_prefix)
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/output.py", line 68, in init
self.dft_info = parse_dft_info(self.filename)
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/block_parser/header_info.py", line 91, in parse_dft_info
return DFTInfo(ks_type=dft_info["ks_type"][0][0][0], multiplicity=dft_info["multiplicity"][0][0][0])
IndexError: list index out of range
(deepmd) xwj@ERNIC:~/materials/water/water-deepmd$ python water-dp.py
--- You are parsing data using package Cp2kData ---
Traceback (most recent call last):
File "/home/xwj/materials/water/water-deepmd/water-dp.py", line 10, in
data = dpdata.LabeledSystem('./{}-dp'.format(file_label), cp2k_output_name = 'md.log', fmt="cp2kdata/md")
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 183, in init
self.from_fmt(
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 220, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, kwargs)
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/dpdata/system.py", line 1113, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, kwargs)
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/dpdata_plugin.py", line 73, in from_labeled_system
cp2kmd = Cp2kOutput(output_file=cp2k_output_name, run_type="MD", path_prefix=path_prefix)
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/output.py", line 68, in init
self.dft_info = parse_dft_info(self.filename)
File "/home/xwj/miniconda3/envs/deepmd/lib/python3.10/site-packages/cp2kdata/block_parser/header_info.py", line 91, in parse_dft_info
return DFTInfo(ks_type=dft_info["ks_type"][0][0][0], multiplicity=dft_info["multiplicity"][0][0][0])
IndexError: list index out of range
I provided my .inp file, the other files are too big for me to upload: water-dp.zip