Add README for documentation.

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.3) # need 3.3 for POLICY CMP0057
+cmake_minimum_required(VERSION 3.5) # need at least 3.3 for POLICY CMP0057
 project(cpptraj NONE)
 
 #version number

appveyor.yml

@@ -1,7 +1,7 @@
 platform:
   - x64
 
-image: Visual Studio 2019
+image: Visual Studio 2015
 
 clone_folder: c:\projects\cpptraj
 

cmake-cpptraj/SetupThirdParty.cmake

@@ -150,7 +150,7 @@ if(NEED_mkl)
 
 	# Static MKL is not the default at this time.
 	# <long_explanation>
-	# MKL has a fftw3 compatibility interface.  Wierdly enough, this interface is spread out between several different libraries: the main interface library, the 
+	# MKL has a fftw3 compatibility interface.  Weirdly enough, this interface is spread out between several different libraries: the main interface library, the
 	# cdft library, and the actual fftw3 interface library (which is distributed as source code, not a binary).
 	# So, even though we don't use the fftw3 interface, there are symbols in the main MKL libraries which conflict with the symbols from fftw3.
 	# Oddly, on many platforms, the linker handles this fine.  However, in at least one case (the SDSC supercomputer Comet, running a derivative of CentOS),
@@ -346,9 +346,9 @@ endif()
 # we can now reset this back to the default behavior -- targets will be made PIC as needed in the individual CMake scripts
 unset(CMAKE_POSITION_INDEPENDENT_CODE)
 
-set(FORCE_EXTERNAL_LIBS "" CACHE STRING "3rd party libraries to force using the system version of. Accepts a semicolon-seperated list of library names from the 3rd Party Libraries section of the build report.")
-set(FORCE_INTERNAL_LIBS "" CACHE STRING "3rd party libraries to force to build inside Amber. Accepts a semicolon-seperated list of library names from the 3rd Party Libraries section of the build report.")
-set(FORCE_DISABLE_LIBS "" CACHE STRING "3rd party libraries to force Amber to not use at all. Accepts a semicolon-seperated list of library names from the 3rd Party Libraries section of the build report.")
+set(FORCE_EXTERNAL_LIBS "" CACHE STRING "3rd party libraries to force using the system version of. Accepts a semicolon-separated list of library names from the 3rd Party Libraries section of the build report.")
+set(FORCE_INTERNAL_LIBS "" CACHE STRING "3rd party libraries to force to build inside Amber. Accepts a semicolon-separated list of library names from the 3rd Party Libraries section of the build report.")
+set(FORCE_DISABLE_LIBS "" CACHE STRING "3rd party libraries to force Amber to not use at all. Accepts a semicolon-separated list of library names from the 3rd Party Libraries section of the build report.")
 
 # look for and handle suspicious tools
 if(NOT TRUST_SYSTEM_LIBS)
@@ -379,39 +379,42 @@ endif()
 foreach(TOOL ${FORCE_EXTERNAL_LIBS})
 	colormsg(YELLOW "Forcing ${TOOL} to be sourced externally")
 
-	list_contains(VALID_TOOL ${TOOL} ${3RDPARTY_TOOLS})
+	string(TOLOWER ${TOOL} TOOL_LOWERCASE)
+	list_contains(VALID_TOOL ${TOOL_LOWERCASE} ${3RDPARTY_TOOLS})
 
 	if(NOT VALID_TOOL)
 		message(FATAL_ERROR "${TOOL} is not a valid 3rd party library name.")
 	endif()
 
-	set_3rdparty(${TOOL} EXTERNAL)
+	set_3rdparty(${TOOL_LOWERCASE} EXTERNAL)
 endforeach()
 
 if(INSIDE_AMBER)
 	foreach(TOOL ${FORCE_INTERNAL_LIBS})
 		colormsg(GREEN "Forcing ${TOOL} to be built internally")
 
-		list_contains(VALID_TOOL ${TOOL} ${3RDPARTY_TOOLS})
+		string(TOLOWER ${TOOL} TOOL_LOWERCASE)
+		list_contains(VALID_TOOL ${TOOL_LOWERCASE} ${3RDPARTY_TOOLS})
 
 		if(NOT VALID_TOOL)
 			message(FATAL_ERROR "${TOOL} is not a valid 3rd party library name.")
 		endif()
 
-		set_3rdparty(${TOOL} INTERNAL)
+		set_3rdparty(${TOOL_LOWERCASE} INTERNAL)
 	endforeach()
 endif()
 
 foreach(TOOL ${FORCE_DISABLE_LIBS})
 	colormsg(HIRED "Forcing ${TOOL} to be disabled")
 
-	list_contains(VALID_TOOL ${TOOL} ${3RDPARTY_TOOLS})
+	string(TOLOWER ${TOOL} TOOL_LOWERCASE)
+	list_contains(VALID_TOOL ${TOOL_LOWERCASE} ${3RDPARTY_TOOLS})
 
 	if(NOT VALID_TOOL)
 		message(FATAL_ERROR "${TOOL} is not a valid 3rd party library name.")
 	endif()
 
-	set_3rdparty(${TOOL} DISABLED)
+	set_3rdparty(${TOOL_LOWERCASE} DISABLED)
 endforeach()
 
 # force all unneeded tools to be disabled

devtools/ci/appveyor/build.bat

@@ -8,7 +8,7 @@ if %BUILD_TYPE% equ cmake-vs (
 	mkdir build
 	cd build
 
-	cmake .. "-GVisual Studio 14 2015 Win64" -DCMAKE_PREFIX_PATH=%PREBUILTS_DIR% -DPRINT_PACKAGING_REPORT=TRUE -DARCHIVE_FORMAT=ZIP -DINSTALL_HEADERS=TRUE -DCOMPILER=AUTO -DCMAKE_INSTALL_PREFIX=%SRCDIR% -DCMAKE_BUILD_TYPE=RELEASE -DUSE_ARPACK=FALSE -DUSE_TNG=FALSE
+	cmake .. "-GVisual Studio 14 2015" -A x64 -DCMAKE_PREFIX_PATH=%PREBUILTS_DIR% -DPRINT_PACKAGING_REPORT=TRUE -DARCHIVE_FORMAT=ZIP -DINSTALL_HEADERS=TRUE -DCOMPILER=AUTO -DCMAKE_INSTALL_PREFIX=%SRCDIR% -DCMAKE_BUILD_TYPE=RELEASE -DUSE_ARPACK=FALSE -DUSE_TNG=FALSE
 	msbuild cpptraj.sln
 	msbuild INSTALL.vcxproj
 	msbuild PACKAGE.vcxproj

doc/README.md

@@ -0,0 +1,8 @@
+Cpptraj Documentation
+=====================
+
+The `GeneratePDFs.sh` script will attempt to build the Cpptraj documentation PDFs from the Lyx files. It requires md5sum and lyx. It checks the md5sum of each lyx file and if it differs from what is in `DocumentChecksums.txt` it will run Lyx to attempt to generate the PDF for that document only. 
+
+If not using `GeneratePDFs.sh` you should ensure the \*.lyx file checksums are up to date in `DocumentChecksums.txt`.
+
+Manual references are stored in `cpptraj.bib` in Bibtex format.

src/helpme_standalone.h

@@ -39,6 +39,7 @@
 #include <tuple>
 #include <unistd.h>
 #include <vector>
+#include <cstdint>
 
 // original file: src/cartesiantransform.h