License changed to BSD 3-clause license

bin/ForceBalance.py

@@ -60,7 +60,7 @@ def process(word, color):
  return Answer
 
 def main():
- printcool("Welcome to ForceBalance version 1.3! =D\nForce Field Optimization System\n\nAuthors:\nLee-Ping Wang\nKeri McKiernan, Yudong Qiu\nArthur Vigil, Erik Brandt, Johnny Israeli", ansi="1", bold=True, minwidth=64)
+ printcool("Welcome to ForceBalance version 1.5.0! =D\nForce Field Optimization System\n\nAuthors:\nLee-Ping Wang\nKeri A. McKiernan, Yudong Qiu\nArthur Vigil, Erik G. Brandt, Johnny Israeli", ansi="1", bold=True, minwidth=64)
  logostr = """
  ,'+++ 
  ,++++++. .:,,. 

doc/api_header.tex

@@ -57,7 +57,7 @@
 \vspace*{1cm}
 \begin{center}
 
-{\Large ForceBalance Developer API Guide version 1.3}\\
+{\Large ForceBalance Developer API Guide version 1.5.0}\\
 \vspace*{2cm}
 {\large Generated by Doxygen 1.8.11}\\
 \vspace*{2.5 cm}

doc/header.tex

@@ -57,7 +57,7 @@
 \vspace*{1cm}
 \begin{center}
 
-{\Large ForceBalance version 1.3}\\
+{\Large ForceBalance version 1.5.0}\\
 \vspace*{2cm}
 {\large Generated by Doxygen 1.8.11}\\
 \vspace*{2.5 cm}

setup.py

@@ -27,9 +27,9 @@
 #| |#
 #| doc/header.tex |#
 #| doc/api_header.tex |#
-#| src/__init__.py  |#
+#| bin/ForceBalance.py |#
 #===================================#
-__version__ = "v1.3.2"
+__version__ = "v1.5.0"
 try:
  # use git to find current version
  git_describe = subprocess.check_output(["git", "describe"]).strip()
@@ -91,7 +91,7 @@ def buildKeywordDictionary(args):
  setupKeywords["version"] = re.sub('-[0-9]*$','',__version__)
  setupKeywords["author"] = "Lee-Ping Wang"
  setupKeywords["author_email"] = "[email protected]"
- # setupKeywords["license"] = "GPL 3.0"
+ setupKeywords["license"] = "BSD 2.0"
  setupKeywords["url"] = "https://simtk.org/home/forcebalance"
  setupKeywords["download_url"] = "https://simtk.org/home/forcebalance"
  setupKeywords["scripts"] = glob.glob("bin/*.py") + glob.glob("bin/*.sh") + glob.glob("bin/*.bash") + glob.glob("bin/ForceBalance") + glob.glob("bin/TidyOutput")

src/data/npt.py

@@ -7,43 +7,8 @@
 or the enthalpy of vaporization) and compute the derivative with respect 
 to changing the force field parameters. This script is a part of ForceBalance.
 
-The basic idea is this: First we run a density simulation to determine
-the average density. This quantity of course has some uncertainty,
-and in general we want to avoid evaluating finite-difference
-derivatives of noisy quantities. The key is to realize that the
-densities are sampled from a Boltzmann distribution, so the analytic
-derivative can be computed if the potential energy derivative is
-accessible. We compute the potential energy derivative using
-finite-difference of snapshot energies and apply a simple formula to
-compute the density derivative.
-
-References
-
-[1] Shirts MR, Mobley DL, Chodera JD, and Pande VS. Accurate and efficient corrections for
-missing dispersion interactions in molecular simulations. JPC B 111:13052, 2007.
-
-[2] Ahn S and Fessler JA. Standard errors of mean, variance, and standard deviation estimators.
-Technical Report, EECS Department, The University of Michigan, 2003.
-
-Copyright And License
-
-@author Lee-Ping Wang <[email protected]>
-@author John D. Chodera <[email protected]> (Wrote statisticalInefficiency and MTS-VVVR)
-
-All code in this repository is released under the GNU General Public License.
-
-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.
-
-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/>.
-
+All code in this repository is released under the BSD 3-Clause License (aka BSD 2.0).
+Please see github.com/leeping/forcebalance for more details.
 """
 from __future__ import division
 

src/data/npt_lipid.py

@@ -1,49 +1,14 @@
 #!/usr/bin/env python
 
 """
-@package npt
+@package npt_lipid
 
 Runs a simulation to compute condensed phase properties (for example, the density 
 or the enthalpy of vaporization) and compute the derivative with respect 
 to changing the force field parameters. This script is a part of ForceBalance.
 
-The basic idea is this: First we run a density simulation to determine
-the average density. This quantity of course has some uncertainty,
-and in general we want to avoid evaluating finite-difference
-derivatives of noisy quantities. The key is to realize that the
-densities are sampled from a Boltzmann distribution, so the analytic
-derivative can be computed if the potential energy derivative is
-accessible. We compute the potential energy derivative using
-finite-difference of snapshot energies and apply a simple formula to
-compute the density derivative.
-
-References
-
-[1] Shirts MR, Mobley DL, Chodera JD, and Pande VS. Accurate and efficient corrections for
-missing dispersion interactions in molecular simulations. JPC B 111:13052, 2007.
-
-[2] Ahn S and Fessler JA. Standard errors of mean, variance, and standard deviation estimators.
-Technical Report, EECS Department, The University of Michigan, 2003.
-
-Copyright And License
-
-@author Lee-Ping Wang <[email protected]>
-@author John D. Chodera <[email protected]> (Wrote statisticalInefficiency and MTS-VVVR)
-
-All code in this repository is released under the GNU General Public License.
-
-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.
-
-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/>.
-
+All code in this repository is released under the BSD 3-Clause License (aka BSD 2.0).
+Please see github.com/leeping/forcebalance for more details.
 """
 from __future__ import division
 

src/data/nvt.py

@@ -4,9 +4,9 @@
 """
 @package nvt
 
-Runs a simulation to compute condensed phase properties in NVT ensemble
-(for example, the surface tension) and compute the derivative with respect
-to changing the force field parameters. This script is a part of ForceBalance.
+Runs a simulation to compute condensed phase properties (for example, the density 
+or the enthalpy of vaporization) and compute the derivative with respect 
+to changing the force field parameters.  This script is a part of ForceBalance.
 
 The algorithm used to compute the surface tension is the test-area method.
 We run a NVT simulation on a film of water in a long PBC box. For each frame, we
@@ -34,20 +34,8 @@
 
 Note: Many parts of this script is directly copied from npt.py
 
-All code in this repository is released under the GNU General Public License.
-
-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.
-
-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/>.
-
+All code in this repository is released under the BSD 3-Clause License (aka BSD 2.0).
+Please see github.com/leeping/forcebalance for more details.
 """
 from __future__ import division
 

src/molecule.py

@@ -6,16 +6,11 @@
 #| Chemical file format conversion module |#
 #| |#
 #| Lee-Ping Wang ([email protected]) |#
-#| Last updated July 5, 2016  |#
+#| Last updated January 22, 2018 |#
 #| |#
-#| This is free software released under version 2 of the GNU GPL, |#
-#| please use or redistribute as you see fit under the terms of |#
-#| this license. (http://www.gnu.org/licenses/gpl-2.0.html) |#
-#| |#
-#| 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. |#
+#| This code is part of ForceBalance and is covered under the |#
+#| ForceBalance copyright notice and BSD 3-clause license. |#
+#| Please see https://github.com/leeping/forcebalance for details. |#
 #| |#
 #| Feedback and suggestions are encouraged. |#
 #| |#
@@ -65,7 +60,9 @@
 #| f) Extra stuff |#
 #| 4) "main" function (if executed) |#
 #| |#
-#| Required: Python 2.7, Numpy 1.6 |#
+#| Required: Python 2.7 or 3.6 |#
+#| (2.6, 3.5 and earlier untested) |#
+#| NumPy 1.6 |#
 #| Optional: Mol2, PDB, DCD readers |#
 #| (can be found in ForceBalance) |#
 #| NetworkX package (for topologies) |#