Merge pull request #62 from giacomofiorin/fix-compiler-warnings

USER-COLVARS package :h4,link(user-colvars)

This package includes into the LAMMPS distribution the Colvars library, which

can be built for the most part with all major versions of the C++ language.

A few of the most recent features require C++11 support.  In particular, the

library is optionally built together with the

"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also

included in the LAMMPS distribution.  Lepton implements the

"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction

feature, and requires C++11 support.

See "here"_https://colvars.github.io/README-c++11.html for a detailed list of

C++11-only features.

[CMake build]:

The USER-COLVARS package requires the use of a C++11 compiler to compile

the included Lepton library. You can set the flag "-D COLVARS_LEPTON=no"

in addition to "-D PKG_USER-COLVARS=yes" in order to instruct CMake to

skip building and including the Lepton library into the USER-COLVARS code.

This is the recommended build recipe: no additional settings are normally

needed besides "-D PKG_USER-COLVARS=yes".

Building and linking of Lepton (or other C++11-only features) is enabled

automatically when compilation is carried out with C++11 support, and disabled

otherwise.  Optionally, Lepton build may be manually controlled with the flag

"-D COLVARS_LEPTON=yes|no".

[Traditional make]:

Before building LAMMPS, you must build the COLVARS library in

lib/colvars.  You can do this manually if you prefer; follow the

instructions in lib/colvars/README.  You can also do it in one step

from the lammps/src dir, using a command like these, which simply

invoke the lib/colvars/Install.py script with the specified args:

Before building LAMMPS, one must build the Colvars library in lib/colvars.

This can be done manually in the same folder by using or adapting one of the

provided Makefiles: for example, Makefile.g++ for the GNU compiler.

In general, it is safer to use build setting consistent with the rest of

LAMMPS.  This is best carried out from the LAMMPS src directory using a

command like these, which simply invoke the lib/colvars/Install.py script with

the specified args:

make lib-colvars                      # print help message

make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")

make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")

make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre

The build should produce two files: lib/colvars/libcolvars.a and

lib/colvars/Makefile.lammps.  The latter is copied from an existing

Makefile.lammps.* and has settings needed to build LAMMPS with the

COLVARS library (though typically the settings are just blank).  If

necessary, you can edit/create a new lib/colvars/Makefile.machine file

for your system, which should define an EXTRAMAKE variable to specify

a corresponding Makefile.lammps.machine file.

The "machine" argument of the "-m" flag is used to find a Makefile.machine to

use as build recipe.  If it does not already exist in lib/colvars, it will be

auto-generated by using compiler flags consistent with those parsed from the

core LAMMPS makefiles.

Optional flags may be specified as environment variables:

COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)

COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)

The build should produce two files: the library lib/colvars/libcolvars.a

(which also includes Lepton objects if enabled) and the specification file

lib/colvars/Makefile.lammps.  The latter is auto-generated, and normally does

not need to be edited.

:line

def get_lammps_machine_flags(machine):

  """Parse Makefile.machine from LAMMPS, return dictionary of compiler flags"""

  if not os.path.exists("../../src/MAKE/MACHINES/Makefile.%s" % machine):

    sys.exit("Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine)

    sys.exit("ERROR: Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine)

  lines = open("../../src/MAKE/MACHINES/Makefile.%s" % machine,

               'r').readlines()

  machine_flags = {}

          (words[0] == 'SHFLAGS') or (words[0] == 'ARCHIVE') or

          (words[0] == 'ARFLAGS') or (words[0] == 'SHELL')):

        machine_flags[words[0]] = ' '.join(words[2:])

  if machine_flags:

    print("Detected the following flags: ", machine_flags)

  return machine_flags

def gen_colvars_makefile_machine(machine, machine_flags):

  machine_flags = get_lammps_machine_flags(machine)

  gen_colvars_makefile_machine(machine, machine_flags)

if not os.path.exists("Makefile.%s" % machine):

  sys.exit("lib/%s/Makefile.%s does not exist" % (lib,machine))

  sys.exit("ERROR: lib/%s/Makefile.%s does not exist" % (lib,machine))

# create Makefile.auto as copy of Makefile.machine

# reset EXTRAMAKE if requested

n_cpus = get_cpus()

print("Building lib%s.a ..." % lib)

cmd = ["make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus]

cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus

try:

  txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True);

  txt = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT);

  print(txt.decode('UTF-8'))

except subprocess.CalledProcessError as e:

  print("Make failed with:\n %s" % e.output.decode('UTF-8'))

  sys.exit(1)

  sys.exit("Make failed with:\n %s" % e.output.decode('UTF-8'))

if os.path.exists("lib%s.a" % lib):

  print("Build was successful")

else:

  sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib, lib))

if os.path.exists("lib%s.a" % lib): print("Build was successful")

else: sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))

if not os.path.exists("Makefile.lammps"):

  print("lib/%s/Makefile.lammps was NOT created" % lib)

  print("WARNING: lib/%s/Makefile.lammps was NOT created" % lib)

# Allow to selectively turn off Lepton

ifeq ($(ENABLE_LEPTON),no)

ifeq ($(COLVARS_LEPTON),no)

LEPTON_INCFLAGS = 

COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o)

else

# -*- makefile -*- to build Colvars module with GNU compiler

COLVARS_DEBUG = "YES"

COLVARS_DEBUG = yes

include Makefile.g++

# -*- makefile -*- to build Colvars module with GNU compiler

COLVARS_LEPTON = no

include Makefile.g++