Merge branch 'master' into devel

.travis.yml

@@ -0,0 +1,35 @@
+sudo: required
+dist: trusty
+language: fortran
+
+matrix:
+ include:
+ - os: linux
+ compiler: clang
+ env: BTYPE=Debug
+ - os: linux
+ compiler: gcc
+ env: BTYPE=Release
+
+before_install:
+ - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get --yes update; fi
+ - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get --yes install gfortran; fi
+ - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get --yes install liblapack-dev; fi
+ - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get --yes install fftw3; fi
+ - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get --yes install libfftw3-dev; fi
+ - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get --yes install python; fi
+
+install:
+ - mkdir pscf-build && cd pscf-build
+ # Configure
+ - cmake $TRAVIS_BUILD_DIR -DCMAKE_Fortran_COMPILER=`which gfortran` -DCMAKE_BUILD_TYPE=$BTYPE -DCMAKE_INSTALL_PREFIX=~/pscf
+ # Build
+ - make
+
+script:
+ ## Test the program
+ #- make test
+ # Create package
+ - make package
+ # Make sure we can install with no issues.
+ - make install

CMakeLists.txt

@@ -1,14 +1,14 @@
 IF (USE_INTEL)
  set (CMAKE_C_COMPILER "icc")
  set (CMAKE_CXX_COMPILER "icpc")
-ENDIF (USE_INTEL) 
+ENDIF (USE_INTEL)
 
 
 # CMakeLists files in this project can
 # refer to the root source directory of the project as ${PSCF_SOURCE_DIR} and
 # to the root binary directory of the project as ${PSCF_BINARY_DIR}.
 cmake_minimum_required (VERSION 2.8.11)
-project (PSCF)
+project (PSCF Fortran)
 
 #### Based on https://cmake.org/Wiki/CMakeForFortranExamplea ####
 enable_language (Fortran)
@@ -75,32 +75,32 @@ set(CPACK_PACKAGE_VERSION_PATCH "0")
 # TODO: build out components "applications libraries headers" (where headers are the .mod files)
 set(CPACK_COMPONENTS_ALL Unspecified)
 
-# DONE: finish Bundle 
+# DONE: finish Bundle
 # DONE: finish DEB and RPM generators (http:https://www.vtk.org/Wiki/CMake:Component_Install_With_CPack)
 # TODO: finish NSIS generator (http:https://www.vtk.org/Wiki/CMake:Component_Install_With_CPack)
 # DONE: test compile and package on Unix and Windows
 if (APPLE)
  if (BUILD_DMG)
- set(CPACK_GENERATOR 
- Bundle 
+ set(CPACK_GENERATOR
+ Bundle
  )
  else (BUILD_DMG)
- set(CPACK_GENERATOR 
+ set(CPACK_GENERATOR
  TGZ
  ZIP
  )
  endif (BUILD_DMG)
 else (APPLE)
  if (UNIX)
  if (EXISTS /etc/redhat-release)
- set(CPACK_GENERATOR 
+ set(CPACK_GENERATOR
  RPM
  TGZ
  ZIP
  )
  set(CPACK_RPM_PACKAGE_REQUIRES "lapack >= 3.0.0, libfft3 >= 3.2.0")
  else()
- set(CPACK_GENERATOR 
+ set(CPACK_GENERATOR
  DEB
  TGZ
  ZIP
@@ -111,8 +111,8 @@ else (APPLE)
  set(CPACK_PACKAGING_INSTALL_PREFIX "/usr/local")
  endif()
  else (UNIX)
- set(CPACK_GENERATOR 
- NSIS 
+ set(CPACK_GENERATOR
+ NSIS
  ZIP
  )
  endif(UNIX)
@@ -128,7 +128,7 @@ set(CPACK_BUNDLE_STARTUP_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/tools/bundle/pscf.s
 #set(CPACK_PACKAGE_ICON ${CMAKE_CURRENT_SOURCE_DIR}/tools/bundle/Icon.png)
 
 set(CPACK_DEBIAN_PACKAGE_MAINTAINER "Evan Bollig") #required for DEB
- 
+
 set(BU_CHMOD_BUNDLE_ITEMS ON)
 set(CPACK_BINARY_DRAGNDROP ON)
 #set(CMAKE_INSTALL_PREFIX ${CMAKE_BINARY_DIR})
@@ -142,7 +142,7 @@ set(CPACK_RESOURCE_FILE_WELCOME ${CMAKE_SOURCE_DIR}/README)
 set(CPACK_PACKAGE_DESCRIPTION_FILE ${CMAKE_SOURCE_DIR}/README)
 
 if (APPLE AND BUILD_DMG)
-# Force the README up to the DMG root 
+# Force the README up to the DMG root
 INSTALL(FILES ${CMAKE_SOURCE_DIR}/README DESTINATION ../../../Extra RENAME README.txt)
 INSTALL(FILES ${CMAKE_SOURCE_DIR}/LICENSE DESTINATION ../../../Extra RENAME LICENSE.txt)
 INSTALL(FILES ${CMAKE_SOURCE_DIR}/tools/bundle/HOWTO_INSTALL_OSX.txt DESTINATION ../../../. RENAME HOWTO_INSTALL_OSX.txt)
@@ -151,7 +151,7 @@ INSTALL(FILES ${CMAKE_SOURCE_DIR}/README DESTINATION share/pscf RENAME README.tx
 INSTALL(FILES ${CMAKE_SOURCE_DIR}/LICENSE DESTINATION share/pscf RENAME LICENSE.txt)
 endif (APPLE AND BUILD_DMG)
 
-install(PROGRAMS 
+install(PROGRAMS
  tools/bin/pscf-read-sweep tools/bin/pscf-env
  DESTINATION bin)
 

Dockerfile

@@ -0,0 +1,36 @@
+# This is the Dockerfile for PSCF.
+#
+# To build the container, you need docker to be installed on
+# your machine (https://www.docker.com) and run the following command
+#
+# docker build -t pscf .
+#
+# It will create a Debian-based container that contains everything
+# needed to compile pscf
+#
+# Everything will be installed in /pscf
+#
+# To run the container interactively
+#
+# docker run -it pcsf /bin/bash
+
+FROM debian
+
+RUN apt-get update && \
+ apt-get install -y \
+ cmake \
+ gfortran \
+ liblapack3 \
+ libfftw3-dev \
+ python
+
+WORKDIR .
+ADD . /pcsf
+RUN cd /pcsf_SRC && \
+ mkdir -p build && \
+ cd build && \
+ export FC=`which gfortran` && \
+ cmake .. -DCMAKE_BUILD_TYPE=Release \
+ -DCMAKE_INSTALL_PREFIX=/pcsf && \
+ make && \
+ make install

README.md

@@ -0,0 +1,72 @@
+# PSCF - Polymer Self-Consistent Field Theory
+
+[![Travis][buildstatus_image_travis]][travisci]
+
+Copyright (2002-2016) Regents of the University of Minnesota
+
+PSCF is a Fortran 90 program for numerically solving the polymer
+self-consistent field theory for periodic microstructures formed
+by incompressible melts or mixtures of linear block copolymers,
+linear homopolymers, and small molecule solvents.
+
+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. A copy of this license is included in
+the LICENSE file in the top-level PSCF directory.
+
+# Contributors
+
+- David Morse
+- Chris Tyler
+- Jian Qin
+- Amit Ranjan
+- Raghuram Thiagarajan
+- Akash Arora
+
+# Dependencies
+
+ PSCF depends upon the FFTW fast Fourier transform library and the
+ LAPACK linear algebra library. These packages must be installed
+ before attempting to compile the program from source.
+
+# User Documentation
+
+A web user manual is avalaible at:
+
+ https://pscf.readthedocs.io
+
+Instructions for compiling the program from source, as well as various
+ways to install precompiled executables, are given in the user manual.
+
+The source files for the user manual are text files that are stored in
+the doc/user-man directory. The relevant files have file extension .rst.
+
+# Developer Documentation
+
+A local copy of the developer API documentation, which includes
+documentation for all modules, subroutines and public variables, may
+be regenerated by following instructions given in the file doc/README.
+The resulting .html page are installed in doc/devel-man.
+
+# Directory Structure
+
+ src/ - Fortran 90 source files
+ doc/ - documentation files
+ doc/user-man - - user manual source files
+ tools/ - Tools for processing output and source
+ tools/matlab - - matlab scripts for visualization
+ tools/python - - python modules
+ make/ - build directory for make
+
+An annotated list of source files is given in the file src/SRC_FILES.
+Before modifying any fortran files, see the note at the end of that
+file regarding the use of preprocessor to generate some files.
+
+# Examples
+
+A library of examples is provided in a separate github repository,
+located at https://github.com/dmorse/pscf-examples
+
+
+[buildstatus_image_travis]: https://travis-ci.org/Gjacquenot/pscf.svg?branch=master
+[travisci]: https://travis-ci.org/Gjacquenot/pscf

doc/user-man/compile-make.rst

@@ -4,11 +4,12 @@
 Compiling from source, using make
 =================================
 
-It is also possible to compile using the unix make utility using a simple
-Makefile that is provided in the make/ directory of the git repository. The 
-instructions for using make to compile from source are same on any unix-like 
-operating system, including Max OS X. The main difference among different 
-unix environments is the locations of the required libraries. 
+It is also possible to compile using the unix make utility alone, using 
+a simple Makefile that is provided in the make/ directory of the git 
+repository. The instructions for using make to compile from source are 
+the same on any unix-like operating system, including Max OS X. The main 
+difference among different unix environments is the locations of the 
+required libraries. 
 
 To compile the code in this way, proceed as follows:
 
@@ -17,33 +18,39 @@ To compile the code in this way, proceed as follows:
  page. You will need to install all dependencies listed there
  except cmake.
 
- * Follow the directions given in the preceding discussion of
- :ref:`install-compile-cmake-getsource-sub` to obtain the source
- code and create an appropriate directory structure.
+ * Follow the directions given in the discussion of
+ :ref:`install-compile-cmake-getsource-sub` on the previous page
+ to create an appropriate directory structure and obtain the 
+ source code. After this step, you should have a directory named
+ pscf/ with a directory named git/ that contains the contents of
+ the git repository. You do not need to create a subdirectory
+ of pscf/ named cmake/ if you are not using cmake.
 
- * Change the working directory (cd) to the directory pscf/git/make in
- the directory structure described in the instructions for compiling
- with cmake. Note that this is an existing subdirectory of the 
- pscf/git directory, and is different from the initially empty 
- pscf/cmake directory from which we recommended that invoke cmake
- when using cmake to generate makefiles.
+ * Change the working directory (cd) to the directory pscf/git/make .
+ Note that this is an existing subdirectory of the pscf/git 
+ directory, and is different from the initially empty directory
+ pscf/cmake from which we recommended that invoke cmake when using 
+ cmake to compile.
 
  * The pscf/git/make directory will contain files named config.mk_r 
  and Makefile. Make a copy of the file config.mk_r, by entering::
 
  cd config.mk_r config.mk
 
  * Examine and edit the new config.mk file to reflect your environment, 
- and to specify an installation directory. The need to manually edit 
- this configuration file is the main difference between using cmake 
- to generate makefiles and using the simple makefile distributed with
- the source code. See below for further instructions about this step.
+ and to specify an installation directory. See below for further 
+ instructions about this step. The need to manually edit this 
+ configuration file is the main difference between using cmake to 
+ generate makefiles and using the simple makefile distributed with
+ the source code. 
 
  * To compile, enter::
 
  > make -j4 all
 
- from within pscf/git/make. The "-j4" option is not necessary.
+ from within pscf/git/make. The "-j4" option is not necessary, and
+ simply installs make to try to use up to 4 CPU cores during
+ compilation, if available.
 
  * To install in the directory specified by the $(INSTALL) makefile 
  variable (as defined in config.mk), enter::
@@ -58,10 +65,10 @@ Several of these steps are discussed in more detail below.
 
 **Editing the config.mk configfuration file**
 
-In the config.mk file in the src/make directory (which you must create 
-by copying config.mk_r), you will need to set values for a set of macro 
-variables to values appropriate to your system. Makefile variables you 
-may need to reset are:
+In the config.mk file in the src/make directory (which you should have
+created by copying config.mk_r), you will need to set values for several
+macro variables to values appropriate to your system. Makefile variables 
+you may need to reset are:
 
  ========= ========================================================
  F90 path to executable for Fortran 90 compiler
@@ -74,8 +81,8 @@ may need to reset are:
  ========= ========================================================
 
 The INSTALL makefile variable in this makefile is equivalent to the 
-MAKE_INSTALL_PREFIX variable that can be passed to cmake when compiling
-using cmake.
+MAKE_INSTALL_PREFIX variable that can be passed to cmake when using
+cmake to create a makefile.
 
 The file config.mk_r is a default makefile that is stored in the 
 repository. We require you to make an operational copy of this, named