Initial release

This is the version corresponding to the original submission of the first
theory/proposal publication.

.gitignore

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+__pycache__
+*.egg-info
+*.h5

Contributors.md

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+This project was started by Muhamed Amin based on ideas and suggestions from
+Jochen Küpper. Jean-Michel Hartmann provided Fortran code, based on the book
+<add>.
+
+
+
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+-->

LICENSE.md

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+# CMIclassirot licensing conditions
+
+CMIclassirot is provided by the CFEL Controlled Molecule Imaging group as is. It is licensed under
+the [GPL v3](./LICENSE-GPLv3.md) with the following additional requirements:
+
+* Its use for scientific work is acknowledged by the appropriate reference in any resulting work,
+  e.g., scientific publication.
+
+* All corrections and enhancements must be contributed back to the development of the package within
+  an appropriate time, i.e., no later than the publication of its first use.
+  Please create a pull request on GitHub (preferred) or send an appropriate patch against the latest
+  program version on the `develop` branch.
+
+See the documentation for a full list of contributors.
+
+
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README.devel.md

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+# Development guidelines
+
+Please follow some simple rules for coding on CMIstark:
+- keep the code consistent across the whole package!
+- use git-flow (the tools and the concept)
+- consistently use two empty lines between functions/methods and three empty
+  lines above a class
+
+
+
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README.md

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-# Classical-Alignment
-Classical Alignment of Molecules and Nanorods
+# Classical-physics simulations of laser alignment
+
+Classical-mechanics simulations of the rotational dynamics of rigid molecules
+and nanoparticles in laser-electric fields.
+
+See the files in `examples/` for a start.
+
+## Installation
+
+
+## Documentation
+
+
+## Citation
+
+When you use this program in scientific work, please cite it as Muhamed Amin,
+Jean-Michel Hartmann, Amit K. Samanta, Jochen Küpper, "Laser-induced alignment
+of nanoparticles and macromolecules for single-particle-imaging applications",
+[arXiv:2306.05870](https://arxiv.org/abs/2306.05870)
+
+
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cmiclassirot/__init__.py

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+# -*- coding: utf-8; fill-column: 120; truncate-lines: t -*-
+#
+# Copyright (C) 2020 Jochen Küpper <[email protected]>
+#
+# This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
+# License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# If you use this programm for scientific work, you must correctly reference it; see LICENSE file for details.
+#
+# This program 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with this program. If not, see
+# <http://www.gnu.org/licenses/>.
+
+__author__ = "Jochen Küpper <[email protected]>"

cmiclassirot/field.py

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+# -*- coding: utf-8; fill-column: 100 -*-
+#
+# This file is part of CMIclassirot -- classical-physics rotational molecular-dynamics simulations
+#
+# This program is free software: you can redistribute it and/or modify it under the terms of the GNU
+# General Public License as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# If you use this programm for scientific work, you must correctly reference it; see LICENSE file
+# for details.
+#
+# This program 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
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with this program. If not,
+# see <http://www.gnu.org/licenses/>.
+
+import numpy as np
+from scipy import interpolate
+from scipy.constants import c, epsilon_0
+from pyquaternion import Quaternion
+
+class Field(object):
+    """Electric field class
+
+    For the beginning, this only implements a simple Gaussian pulse (in field strengths!) centered
+    at t=0 and along `Z`.
+
+    .. todo:: Keep in mind that we want to be able to represent elliptically polaerized field by their envelope.
+
+    """
+
+    def __init__(self, amplitude=1.e15, sigma=1.e-9, mean=5.e-9, 
+                 intensity=True, filename=None, dc=None):
+        self.amplitude = amplitude
+        self.sigma = sigma
+        self.Ez = np.array([0., 0., 1.])
+        self.from_file = None
+        self.intensity = intensity
+        self.mu = mean
+        self.dc = dc
+        if filename is not None:
+            f = open(filename)
+            E=[]
+            t=[]
+            for i in f:
+                token = i.split()
+                t.append(float(token[0]))
+                E.append(float(token[1]))
+            t = np.array(t)
+            E = np.array(E)
+            self.from_file = interpolate.interp1d(t,E)
+
+    def __call__(self, t):
+        """Field at time t
+
+        :return: Field vector at time
+        """
+        if self.dc is not None:
+            if t > self.dc[0] and t < self.dc[1]:
+                return self.convert(self.dc[2])
+            else:
+                return 0
+
+        if self.from_file is None:
+            E = self.amplitude * np.exp(-0.5 * ((t-self.mu)/self.sigma)**2)
+            if self.intensity:
+                return self.convert(E)
+            else:
+                return E
+        else:
+            try:
+                E = 1.e16*self.from_file(t)
+                if self.intensity:
+                    return self.convert(E)
+                else:
+                    return E
+            except:
+                return 0.
+
+    def convert(self, I):
+        """ Converts intensity to electric field"""
+        return np.sqrt(2*I/(c * epsilon_0))
+
+    def rotate(self, quaternion=Quaternion()):
+        """Rotate field
+
+        This is used in the actual propagation step, as it is easier/cheaper to rotate the field
+        than to rotate the molecule
+
+        :param rotation: Define the rotation to be applied to the field, as an :class:`Quarternion`
+
+        """
+        return quaternion.rotate(self.Ez)

cmiclassirot/postprocessing.py

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+# -*- coding: utf-8; fill-column: 100 -*-
+#
+# This file is part of CMIclassirot -- classical-physics rotational molecular-dynamics simulations
+#
+# This program is free software: you can redistribute it and/or modify it under the terms of the GNU
+# General Public License as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# If you use this programm for scientific work, you must correctly reference it; see LICENSE.md file
+# for details.
+#
+# This program 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
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with this program. If not,
+# see <http://www.gnu.org/licenses/>.
+
+
+import numpy as np
+
+
+class Expectation(object):
+    """Calculate expectation values of a probability density function given as an :class:`Ensemble`
+
+    .. todo:: implement
+
+    """
+
+    def __init__(self, Ensemble):
+        pass
+
+    def __call__(self):
+        pass
+
+
+class cos2theta(Expectation):
+    pass
+
+
+class cos2theta_2D(Expectation):
+    pass
+
+
+
+class ProbabilityGraphics(object):
+    """Create a graphical representation of a probability density function
+
+    This Object requires a (variable dimension) probability density function and provides various
+    graphical outputs, such as actual 3D images/VRML graphs, contour plots of projections, etc.
+
+    .. todo:: implement
+
+    """
+
+    def __init__(self):
+        pass
+
+
+
+class Projection(object):
+    """Project a probability distribution onto a plane or line
+
+    This object takes a 3D PDF and creates a lower-dimension PDF by projection onto an arbitrary
+    plane or line.
+
+    .. todo:: Discuss how this blends into :class:`Ensemble` and the funtionality in this file: For
+    instance, will we just create a new Ensemble with certain restrictions or in fact create an
+    independent data structure?
+
+    .. todo:: implement
+
+    """
+
+    def __init__(self):
+        pass