Commit 2abd5ad2 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'integration' into small-doc-fixes

parents 29e480ad 1c3302d1

doc/html/Section_start.html

+8 −0
Original line number Diff line number Diff line
@@ -389,6 +389,7 @@ within the LAMMPS code. The options that are currently recogized are:</p> 
<li>-DLAMMPS_BIGBIG</li>

<li>-DLAMMPS_SMALLSMALL</li>

<li>-DLAMMPS_LONGLONG_TO_LONG</li>

<li>-DLAMMPS_EXCEPTIONS</li>

<li>-DPACK_ARRAY</li>

<li>-DPACK_POINTER</li>

<li>-DPACK_MEMCPY</li>
@@ -457,6 +458,13 @@ be compiled with the same setting, or the link will fail.</p> 
MPI version does not recognize &#8220;long long&#8221; data types.  In this case a

&#8220;long&#8221; data type is likely already 64-bits, in which case this setting

will convert to that data type.</p>

<p>The -DLAMMPS_EXCEPTIONS setting can be used to activate alternative

versions of error handling inside of LAMMPS.  This is useful when

external codes drive LAMMPS as a library.  Using this option, LAMMPS

errors do not kill the caller.  Instead, the call stack is unwound and

control returns to the caller.  The library interface provides the

lammps_has_error() and lammps_get_last_error_message() functions to

detect and find out more about a LAMMPS error.</p>

<p>Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY

options can make for faster parallel FFTs (in the PPPM solver) on some

platforms.  The -DPACK_ARRAY setting is the default.  See the

doc/src/Section_start.txt

+9 −0
Original line number Diff line number Diff line
@@ -262,6 +262,7 @@ within the LAMMPS code. The options that are currently recogized are: 
-DLAMMPS_BIGBIG

-DLAMMPS_SMALLSMALL

-DLAMMPS_LONGLONG_TO_LONG

-DLAMMPS_EXCEPTIONS

-DPACK_ARRAY

-DPACK_POINTER

-DPACK_MEMCPY :ul
@@ -334,6 +335,14 @@ MPI version does not recognize "long long" data types. In this case a 
"long" data type is likely already 64-bits, in which case this setting

will convert to that data type.



The -DLAMMPS_EXCEPTIONS setting can be used to activate alternative

versions of error handling inside of LAMMPS.  This is useful when

external codes drive LAMMPS as a library.  Using this option, LAMMPS

errors do not kill the caller.  Instead, the call stack is unwound and

control returns to the caller.  The library interface provides the

lammps_has_error() and lammps_get_last_error_message() functions to

detect and find out more about a LAMMPS error.



Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY

options can make for faster parallel FFTs (in the PPPM solver) on some

platforms.  The -DPACK_ARRAY setting is the default.  See the

python/lammps.py

+50 −0
Original line number Diff line number Diff line
@@ -150,6 +150,11 @@ class lammps(object): 
    if cmd: cmd = cmd.encode()

    self.lib.lammps_command(self.lmp,cmd)



    if self.lib.lammps_has_error(self.lmp):

      sb = create_string_buffer(100)

      self.lib.lammps_get_last_error_message(self.lmp, sb, 100)

      raise Exception(sb.value.decode().strip())



  def extract_global(self,name,type):

    if name: name = name.encode()

    if type == 0:
@@ -304,6 +309,9 @@ class OutputCapture(object): 


  def __exit__(self, type, value, tracebac):

    os.dup2(self.stdout, self.stdout_fd)

    os.close(self.stdout)

    os.close(self.stdout_pipe_read)

    os.close(self.stdout_pipe_write)



  # check if we have more to read from the pipe

  def more_data(self, pipe):
@@ -345,8 +353,11 @@ class AtomList(object): 
  def __init__(self, lammps_wrapper_instance):

    self.lmp = lammps_wrapper_instance

    self.natoms = self.lmp.system.natoms

    self.dimensions = self.lmp.system.dimensions



  def __getitem__(self, index):

    if self.dimensions == 2:

        return Atom2D(self.lmp, index + 1)

    return Atom(self.lmp, index + 1)
@@ -377,6 +388,12 @@ class Atom(object): 
            self.lmp.eval("y[%d]" % self.index),

            self.lmp.eval("z[%d]" % self.index))



  @position.setter

  def position(self, value):

     self.lmp.set("atom", self.index, "x", value[0])

     self.lmp.set("atom", self.index, "y", value[1])

     self.lmp.set("atom", self.index, "z", value[2])



  @property

  def velocity(self):

    return (self.lmp.eval("vx[%d]" % self.index),
@@ -394,6 +411,31 @@ class Atom(object): 
    return self.lmp.eval("q[%d]" % self.index)





class Atom2D(Atom):

  def __init__(self, lammps_wrapper_instance, index):

    super(Atom2D, self).__init__(lammps_wrapper_instance, index)



  @property

  def position(self):

    return (self.lmp.eval("x[%d]" % self.index),

            self.lmp.eval("y[%d]" % self.index))



  @position.setter

  def position(self, value):

     self.lmp.set("atom", self.index, "x", value[0])

     self.lmp.set("atom", self.index, "y", value[1])



  @property

  def velocity(self):

    return (self.lmp.eval("vx[%d]" % self.index),

            self.lmp.eval("vy[%d]" % self.index))



  @property

  def force(self):

    return (self.lmp.eval("fx[%d]" % self.index),

            self.lmp.eval("fy[%d]" % self.index))





class PyLammps(object):

  """

  More Python-like wrapper for LAMMPS (e.g., for iPython)
@@ -603,6 +645,10 @@ class PyLammps(object): 
      with OutputCapture() as capture:

        self.lmp.command(' '.join(cmd_args))

        output = capture.output



      if 'verbose' in kwargs and kwargs['verbose']:

        print(output)



      lines = output.splitlines()



      if len(lines) > 1:
@@ -657,3 +703,7 @@ class IPyLammps(PyLammps): 
    self.write_dump(*cmd_args)

    from IPython.core.display import Image

    return Image('snapshot.png')



  def video(self, filename):

    from IPython.display import HTML

    return HTML("<video controls><source src=\"" + filename + "\"></video>")

src/error.cpp

+61 −1
Original line number Diff line number Diff line
@@ -13,6 +13,7 @@ 


#include <mpi.h>

#include <stdlib.h>

#include <string.h>

#include "error.h"

#include "universe.h"

#include "output.h"
@@ -21,7 +22,7 @@ using namespace LAMMPS_NS; 


/* ---------------------------------------------------------------------- */



Error::Error(LAMMPS *lmp) : Pointers(lmp) {}

Error::Error(LAMMPS *lmp) : Pointers(lmp), last_error_message(NULL) {}



/* ----------------------------------------------------------------------

   called by all procs in universe
@@ -47,8 +48,14 @@ void Error::universe_all(const char *file, int line, const char *str) 
  }

  if (universe->ulogfile) fclose(universe->ulogfile);



#ifdef LAMMPS_EXCEPTIONS

  char msg[100];

  sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line);

  throw LAMMPSException(msg);

#else

  MPI_Finalize();

  exit(1);

#endif

}



/* ----------------------------------------------------------------------
@@ -61,7 +68,14 @@ void Error::universe_one(const char *file, int line, const char *str) 
  if (universe->uscreen)

    fprintf(universe->uscreen,"ERROR on proc %d: %s (%s:%d)\n",

            universe->me,str,file,line);



#ifdef LAMMPS_EXCEPTIONS

  char msg[100];

  sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line);

  throw LAMMPSAbortException(msg, universe->uworld);

#else

  MPI_Abort(universe->uworld,1);

#endif

}



/* ----------------------------------------------------------------------
@@ -95,6 +109,16 @@ void Error::all(const char *file, int line, const char *str) 
    if (logfile) fprintf(logfile,"ERROR: %s (%s:%d)\n",str,file,line);

  }



#ifdef LAMMPS_EXCEPTIONS

  char msg[100];

  sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line);



  if (universe->nworlds > 1) {

    throw LAMMPSAbortException(msg, universe->uworld);

  }



  throw LAMMPSException(msg);

#else

  if (output) delete output;

  if (screen && screen != stdout) fclose(screen);

  if (logfile) fclose(logfile);
@@ -102,6 +126,7 @@ void Error::all(const char *file, int line, const char *str) 
  if (universe->nworlds > 1) MPI_Abort(universe->uworld,1);

  MPI_Finalize();

  exit(1);

#endif

}



/* ----------------------------------------------------------------------
@@ -121,7 +146,14 @@ void Error::one(const char *file, int line, const char *str) 
    if (universe->uscreen)

      fprintf(universe->uscreen,"ERROR on proc %d: %s (%s:%d)\n",

              universe->me,str,file,line);



#ifdef LAMMPS_EXCEPTIONS

  char msg[100];

  sprintf(msg, "ERROR on proc %d: %s (%s:%d)\n", me, str, file, line);

  throw LAMMPSAbortException(msg, world);

#else

  MPI_Abort(world,1);

#endif

}



/* ----------------------------------------------------------------------
@@ -165,3 +197,31 @@ void Error::done(int status) 
  MPI_Finalize();

  exit(status);

}



/* ----------------------------------------------------------------------

   return the last error message reported by LAMMPS (only used if

   compiled with -DLAMMPS_EXCEPTIONS)

------------------------------------------------------------------------- */



char * Error::get_last_error() const

{

  return last_error_message;

}





/* ----------------------------------------------------------------------

   set the last error message (only used if compiled with

   -DLAMMPS_EXCEPTIONS)

------------------------------------------------------------------------- */



void Error::set_last_error(const char * msg)

{

  delete [] last_error_message;



  if(msg) {

    last_error_message = new char[strlen(msg)+1];

    strcpy(last_error_message, msg);

  } else {

    last_error_message = NULL;

  }

}

src/error.h

+34 −0
Original line number Diff line number Diff line
@@ -15,10 +15,41 @@ 
#define LMP_ERROR_H



#include "pointers.h"

#include <string>

#include <exception>



namespace LAMMPS_NS {



class LAMMPSException : public std::exception

{

public:

  std::string message;



  LAMMPSException(std::string msg) : message(msg) {

  }



  ~LAMMPSException() throw() {

  }



  virtual const char * what() const throw() {

    return message.c_str();

  }

};



class LAMMPSAbortException : public LAMMPSException {

public:

  MPI_Comm universe;



  LAMMPSAbortException(std::string msg, MPI_Comm universe) :

    LAMMPSException(msg),

    universe(universe)

  {

  }

};



class Error : protected Pointers {

  char * last_error_message;



 public:

  Error(class LAMMPS *);
@@ -31,6 +62,9 @@ class Error : protected Pointers { 
  void warning(const char *, int, const char *, int = 1);

  void message(const char *, int, const char *, int = 1);

  void done(int = 0); // 1 would be fully backwards compatible



  char * get_last_error() const;

  void   set_last_error(const char * msg);

};



}

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