imce 1.0.0__py3-none-any.whl

imce/__about__.py

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+'''
+This file is part of imce - a simple framework for molecular Monte Carlo sampling with uncertainty quantification.
+
+Copyright (c) 2021 - 2026 Erik Tsvetaev and Christoph Jacob.
+
+imce is free software: you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+imce is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with imce. If not, see <https://www.gnu.org/licenses/>.
+'''
+
+__version__ = '1.0.0'

imce/__init__.py

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+'''
+This file is part of imce - a simple framework for molecular Monte Carlo sampling with uncertainty quantification.
+
+Copyright (c) 2021 - 2026 Erik Tsvetaev and Christoph Jacob.
+
+imce is free software: you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+imce is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with imce. If not, see <https://www.gnu.org/licenses/>.
+'''
+
+from pathlib import Path
+from importlib.resources import files
+import logging
+
+from imce.structure import simbox
+from imce.simulation import mrt2, uqmc
+from imce.energy import xtb_std2_itrf
+from imce.analysis import analysis
+
+import numpy as np
+
+def home() -> Path:
+    return Path(files("imce")).resolve()
+
+logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s] %(message)s",  handlers=[logging.StreamHandler()])
+
+class settings:
+    '''
+    This class holds the generic data for the simulation, that can be accessed from any other class. 
+    
+    It should be defined at the beginning of each run 
+    script and will be handed over to every simulation etc.
+    '''
+    
+    def __init__(self, itrf, windows = [[]], seed = None, unit = 'eV', convolution_factor = None):
+        '''
+        The unit system that the code runs on. Can be either au, eV, nm or cm-1.
+        '''
+
+        from .units import au_to_ev, au_to_nm, au_to_cm1, ev_to_au, cm1_to_au
+        
+        self.create_generator(seed = seed)
+        self.itrf = itrf
+        self.unit = unit # this decides, in which unit the windows, convolution factors and so on are given in
+        
+        if self.unit == 'cm-1':
+            self.convert_to_input = cm1_to_au
+            self.convert_to_output = au_to_cm1
+        elif self.unit == 'nm':
+            self.convert_to_input = nm_to_au
+            self.convert_to_output = au_to_nm
+        elif self.unit == 'eV':
+            self.convert_to_input = ev_to_au
+            self.convert_to_output = au_to_ev
+        elif self.unit == 'au':
+            self.convert_to_input = lambda au : au
+            self.convert_to_output = lambda au : au
+        else:
+            raise imceError('Unit not known')
+
+        self.windows = self.convert_to_input(windows)
+        
+        if convolution_factor is not None:
+            self.convolution_factor = self.convert_to_input(convolution_factor)
+        else:
+            self.convolution_factor = None
+
+        self.itrf.set_convolution_factor(self.convolution_factor)
+
+    def get_windows(self):
+        return self.windows
+
+    def get_convolution_factor(self):
+        return self.convolution_factor
+        
+    def create_generator(self, seed=None):
+        '''
+        This sets the statistical generator used for MC and MD, velocity generation, etc.
+        
+        If a seed is given, the value will be used. If no seed is given, this function generates a random integer and 
+        feeds that into a generator. This is done, so that always one single quotable seed is available to 
+        reproduce the simulation and compare different versions of the code.
+        ''' 
+        self.seed = seed
+        
+        if seed is not None:
+            self.generator = np.random.default_rng(seed)
+        elif seed is None:
+            self.seed = np.random.randint(0, 2147483648) # Minimum and maximum of a python integer
+            self.generator = np.random.default_rng(self.seed)
+        else:
+            raise imceError('Something is not right')
+    
+    def get_generator(self):
+        return self.generator