dynx 2.10__py3-none-any.whl

DynX/__init__.py

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+"""
+========== v1.1
+
+1. Add new parameters: atoms_register_mode, sites_register_mode, using_atoms_cache, using_sites_cache
+2. Now support three modes for registering sites or atoms:
+    a. each worker compares and register items simultaneously; (register)
+    b. each worker compares items firstly, then results are analysised and registered by main process; (remove)
+    c. each worker registers items directly, do not compare; (all)
+3. Choose to use cache or not
+
+========== v1.2
+
+1. Avoid generating debug.log timer.log and dynx.log file when directly import modules from DynX.
+
+========== v2.0
+
+1. Write NetX class to save reaction networks of states, atoms and sites.
+2. Rename RegisterWorker to CompareWorker, part of codes are moved to other module.
+3. Write Register class to register states specifically.
+4. Support generating new states by atoms network and sites network.
+5. Fix bugs.
+
+========== v2.1
+
+1. Fix bugs of load networks.
+2. Add reconstructing atoms networks and sites networks function.
+
+========== v2.2
+
+1. Fix bugs while using kdb method.
+2. Deal with error while using explorer workers. 
+
+========== v2.3
+
+1. Add command line interface (CLI).
+2. Add pyproject.toml configuration file.
+
+========== v2.4
+
+1. Add command line interface rate and event.
+2. Fix nnsites explorer bugs.
+
+========== v2.5
+
+1. Add/update CLI of state and event.
+2. Use numpy.memmap to store state and event record.
+3. Use pathlib.Path to manipulate file path.
+4. Read memmap file dynamically.
+
+========== v2.6
+
+1. Adjust parameters n_state and n_event to adjust state map dynamically.
+2. Add command to show storage of state and event map.
+
+========== v2.7
+
+1. Add CLI of net command.
+2. Fix rewrite sites bug.
+3. Check if file or directory exists when using CLI in case of generating unnecessary objects.
+4. Delete unnecessary config parameters.
+5. Restart from a breaking running will not change the results.
+
+========== v2.8
+
+1. Add worker.get_unique_prod_sites_ids method to generate consistent surface sites for each new atoms.
+2. Plot visited code with ligthgreen and unvisited code with lightblue.
+3. Add parameter skip_double_count choose to skip double count or not.
+
+========== v2.9
+
+1. Add worker.get_optimize_site_atoms_bank method to generate consistent optimized surface atoms for each new sites.
+2. Add SurfaceSites.get_adatom_substrate_sites method to identify substrate sites of adatoms.
+
+========== v2.10
+
+1. Using register class to update the rate list of KMC.
+2. Add key of 'by' in event class to distinguish the generator of events.
+3. Register event for visited atoms and visited sites.
+4. Identify adatoms substrate sites in SurfaceSites class.
+"""
+__VERSION__ = "2.10"
+__DB__ = "sqlite3"
+
+### utilities
+from .utilities.logger import getLogger, writeSysInfo
+from .utilities.timer import Timer
+from .utilities.netx import NetX
+if __DB__ == "sqlite3":
+    from .utilities.db.sql3 import DB
+elif __DB__ == 'lmdb':
+    try:
+        from .utilities.db.lmdb import DB
+    except Exception as e:
+        raise Exception(e)
+else:
+    raise ValueError('Unexpected DB type: {}'.format(__DB__))
+
+### explorer
+from .explorer.explorer import Explorer
+from .explorer.md import MD
+from .explorer.ts_search import TSSearch
+from .explorer.dimer import Dimer
+from .explorer.nnsites import NNSites
+from .explorer.compare import Compare
+
+### Rate
+from .rate.rate import Rate
+from .rate.species import Species
+
+### scenarios
+from .scenarios.local_env import find_local_environments
+
+### Site
+from .sites.site import Site
+from .sites.site_event import SiteEvent, GasAdsDesEvent
+from .sites.site_system import SiteSystem
+from .sites.surf_sites import SurfaceSites
+
+from .structure import unfold_local_environment_new, match
+from .confidence import get_confidence
+from .calculator import CalcProfiler
+from .matcher import MatchProfiler
+from .optimizer import OptProfiler
+from .config import ConfigClass
+from .register import Register
+from .seed import Seed
+from .state import State
+from .event import Event
+from .kdb import KDB
+from .kmc import KMC
+from .workers import Workers
+from .akmc import AKMC
+from .dynx_runner import dynxRunner

DynX/cli/main.py

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+import argparse, sys
+from DynX.cli.akmc import AKMCCommand
+from DynX.cli.clear import ClearCommand
+from DynX.cli.view import ViewCommand
+from DynX.cli.rate import RateCommand
+from DynX.cli.event import EventCommand
+from DynX.cli.db import DBCommand
+from DynX.cli.state import StateCommand
+from DynX.cli.network import NetworkCommand
+from DynX import getLogger, writeSysInfo
+
+
+COMMANDS = [
+    AKMCCommand,
+    ClearCommand,
+    ViewCommand,
+    RateCommand,
+    StateCommand,
+    EventCommand,
+    DBCommand,
+    NetworkCommand,
+]
+
+
+def main():
+    sys.stdout.reconfigure(line_buffering=True)    ### set stdout unbuffered
+
+    parser = argparse.ArgumentParser(prog="dynx")
+    subparsers = parser.add_subparsers(dest="command")
+
+    # regsiter all commands
+    for cmd in COMMANDS:
+        cmd.add_parser(subparsers)
+
+    args = parser.parse_args()
+
+    if args.command is None:
+        print_logo_info()
+        parser.print_help()
+        return
+
+    # execute
+    cmd_class = args.command_class()
+    cmd_class.run(args)
+
+
+def print_logo_info():
+    logger = getLogger()
+    writeSysInfo(logger)
+    logger.info("="*85)
+    logger.info(f"{'DynX: Adaptive kinetic monte carlo simulations &&':^85}")
+    logger.info(f"{'Automatic exploring reaction networks.':^85}")
+    logger.info("="*85)
+
+
+if __name__ == "__main__":
+    main()

DynX/utilities/logger.py

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+import sys, os
+import platform, socket, re, uuid, subprocess
+import logging
+from DynX import __VERSION__
+
+logo =\
+"""
+                                                                                    
+DDDDDDDDDDDDD                                                  XXXXXXX       XXXXXXX
+D::::::::::::DDD                                               X:::::X       X:::::X
+D:::::::::::::::DD                                             X:::::X       X:::::X
+DDD:::::DDDDD:::::D                                            X::::::X     X::::::X
+  D:::::D    D:::::Dyyyyyyy           yyyyyyynnnn  nnnnnnnn    XXX:::::X   X:::::XXX
+  D:::::D     D:::::Dy:::::y         y:::::y n:::nn::::::::nn     X:::::X X:::::X   
+  D:::::D     D:::::D y:::::y       y:::::y  n::::::::::::::nn     X:::::X:::::X    
+  D:::::D     D:::::D  y:::::y     y:::::y   nn:::::::::::::::n     X:::::::::X     
+  D:::::D     D:::::D   y:::::y   y:::::y      n:::::nnnn:::::n     X:::::::::X     
+  D:::::D     D:::::D    y:::::y y:::::y       n::::n    n::::n    X:::::X:::::X    
+  D:::::D     D:::::D     y:::::y:::::y        n::::n    n::::n   X:::::X X:::::X   
+  D:::::D    D:::::D       y:::::::::y         n::::n    n::::nXXX:::::X   X:::::XXX
+DDD:::::DDDDD:::::D         y:::::::y          n::::n    n::::nX::::::X     X::::::X
+D:::::::::::::::DD           y:::::y           n::::n    n::::nX:::::X       X:::::X
+D::::::::::::DDD            y:::::y            n::::n    n::::nX:::::X       X:::::X
+DDDDDDDDDDDDD              y:::::y             nnnnnn    nnnnnnXXXXXXX       XXXXXXX
+                          y:::::y                                                   
+                         y:::::y                                                    
+                        y:::::y                                                     
+                       y:::::y                                                      
+                      yyyyyyy                                                       
+                                                                                    
+"""
+
+def getLogger(name="DynX",
+              logfile=None,
+              fmt="%(message)s",
+              level=logging.INFO):
+    logger = logging.getLogger(name)
+    logger.setLevel(level)
+
+    if logger.handlers:
+        return logger
+
+    formatter = logging.Formatter(fmt, datefmt="%Y-%m-%d %H:%M:%S")
+
+    if logfile is not None:
+        file_handler = logging.FileHandler(logfile)
+        file_handler.setFormatter(formatter)
+        logger.addHandler(file_handler)
+    else:
+        console_handler = logging.StreamHandler(sys.stdout)
+        console_handler.setFormatter(formatter)
+        logger.addHandler(console_handler)
+
+    return logger
+
+def writeSysInfo(logger):
+    logger.info(logo)
+    getSystemInfo(logger)
+
+def getProcessorName():
+    if platform.system() == "Windows":
+        return platform.processor()
+    elif platform.system() == "Darwin":
+        os.environ['PATH'] = os.environ['PATH'] + os.pathsep + '/usr/sbin'
+        command ="sysctl -n machdep.cpu.brand_string"
+        return subprocess.check_output(command).strip()
+    elif platform.system() == "Linux":
+        command = "grep model /proc/cpuinfo"
+        all_info = subprocess.check_output(command, shell=True).decode('utf-8').strip()
+        for line in all_info.split("\n"):
+            if "model name" in line:
+                return re.sub(".*model name.*:", "", line,1)
+    return ""
+
+def getSystemInfo(logger=None):
+    if logger is None:
+      sys.stderr('No logger is provided')
+    try:
+        logger.info('Platform:            %s', platform.system())
+        logger.info('Platform-release:    %s', platform.release())
+        logger.info('Platform-version:    %s', platform.version())
+        logger.info('Architecture:        %s', platform.machine())
+        logger.info('Hostname:            %s', socket.gethostname())
+        logger.info('IP-address:          %s', socket.gethostbyname(socket.gethostname()))
+        logger.info('MAC-address:         %s', ':'.join(re.findall('..', '%012x' % uuid.getnode())))
+        logger.info('Processor:          %s', getProcessorName())
+        logger.info('Version:             %s', __VERSION__)
+        #logger.info('Ram:                 %s', str(round(psutil.virtual_memory().total / (1024.0 **3)))+" GB")
+    #except Exception as e:
+    #    sys.stderr(e)
+    except:
+        pass
+

dynx-2.10.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: dynx
+Version: 2.10
+Summary: Adaptive dynamic kinetic monte carlo simulation & automatic exploration of chemical reaction networks
+Author: Jun Luo
+Project-URL: Homepage, https://gitee.com/aicatal/DynX/tree/v2.0/
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=2.2.5
+Requires-Dist: scipy>=1.15.3
+
+
+
+<p align="center">
+  <img src="./logo.png" alt="logo" width="50%" height="50%"> 
+</p>
+
+# <center> DynX : Extending Time and Spatial Scale of Dynamics Simulations <center>
+
+On-the-fly KMC simulation software based on [ASE](https://wiki.fysik.dtu.dk/ase/index.html) (Atomic Simulation Environment) providing automation saddle searching capabilities. Enable Extending Time and Spatial Scale of Dynamics Simulations. 
+
+## Features
+* Based on the ASE package, supports different calculators such as [PyNEP](https://github.com/bigd4/PyNEP), [PyAMFF](https://gitlab.com/pyamff/pyamff), [DP](https://github.com/deepmodeling/deepmd-kit)(todo), and [LAMMPS](https://www.lammps.org/).
+
+* Allow for automated batch calculations of transition state searching.
+* Main feature: on-the-fly KMC simulation, hyperdynamics...
+
+
+## Installation
+```shell
+$ pip install dynx
+```
+
+### Requirements
+
+|  Package  | version |
+|  ----  | ----  |
+| [Python](https://www.python.org/) | >=     3.8 |
+| [ase](https://wiki.fysik.dtu.dk/ase/index.html)|>=     3.18.0|
+| [Pytorch](https://pytorch.org/)| newest |
+| [PyYAML](https://pyyaml.org/) | newest |
+| [lammps](https://docs.lammps.org/Install_conda.html) |optional|
+| [PyAmff](https://pyamff.gitlab.io/pyamff/main.html#main) |optional|
+| [PyNEP](https://github.com/bigd4/PyNEP) |optional |
+
+
+ ### From Source
+
+```shell
+$ git clone --recursive git@gitlab.com:ai-ltdynamics/DynX.git
+$ cd DynX 
+$ pip install .
+```
+
+
+## Usage
+Go to examples/xxx and simply type
+```shell
+$ dynx run
+```
+Clean the dynx output, please type
+```shell
+$ dynx clear
+```

dynx-2.10.dist-info/RECORD

@@ -0,0 +1,8 @@
+DynX/__init__.py,sha256=UUJUP78Tw9eQP1IbCa6mojUWre3HPit-bPSTr-cKhig,4135
+DynX/cli/main.py,sha256=rCEhhd6s79-dWZYsIOat1rkKNvyK0147Xoa1q1-wlQw,1332
+DynX/utilities/logger.py,sha256=NS00JIeWk7kDM6jWULaPRPJ_OyLA8VqHglWi3pCXQAo,4403
+dynx-2.10.dist-info/METADATA,sha256=v_-uNhwp-LiNX_bVVPjzI0cUd5bWFMakSM6b0IDDxI8,1928
+dynx-2.10.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+dynx-2.10.dist-info/entry_points.txt,sha256=RIakNF-qO0R_fweMIswss_Eq4pkYN0099pw9midEfng,44
+dynx-2.10.dist-info/top_level.txt,sha256=u_hMq3lsHBrtwrqS3EwzXrazVP_A7GxAozduRRpScag,5
+dynx-2.10.dist-info/RECORD,,

dynx-2.10.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

dynx-2.10.dist-info/entry_points.txt

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+[console_scripts]
+dynx = DynX.cli.main:main

dynx-2.10.dist-info/top_level.txt

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+DynX