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Re: [ESPResSo-users] Espressomd-users Digest, Vol 11, Issue 3

From: Nicola Fortunati
Subject: Re: [ESPResSo-users] Espressomd-users Digest, Vol 11, Issue 3
Date: Tue, 27 Sep 2011 12:16:14 +0200
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Il 06/09/2011 18:00, address@hidden ha scritto: 
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Today's Topics:

   1. ADRess trouble (Nicola Fortunati)
   2. Re: ADRess trouble (Olaf Lenz)


----------------------------------------------------------------------

Message: 1
Date: Tue, 06 Sep 2011 09:55:49 +0200
From: Nicola Fortunati <address@hidden>
To: address@hidden
Subject: [ESPResSo-users] ADRess trouble
Message-ID: <address@hidden>
Content-Type: text/plain; charset="iso-8859-15"; Format="flowed"

Hi Espresso users,

i want to install *ADRESS FEATURE* in my *ESPRESSO CODE*.
After *compile*, *make* and *make check* i tested Adress tcl script and 
ESPRESSO returned this message:

address@hidden espresso-3.0.1]# ./Espresso ./samples/adress/Adress_t.tcl
0: Script directory: /home/nicolafortunati/Scrivania/espresso-3.0.1/scripts
*******************************************************
*                                                     *
*                    - ESPResSo -                     *
*                    ============                     *
*        A Parallel Molecular Dynamics Program        *
*                                                     *
* (c) 2010,2011                                       *
* The ESPResSo project                                *
*                                                     *
* (c) 2002,2003,2004,2005,2006,2007,2008,2009,2010    *
* Max-Planck-Institute for Polymer Research           *
* Mainz, Germany                                      *
*                                                     *
*******************************************************

ESPResSo 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.

ESPResSo 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/>.


=======================================================
=              Script:  Adress_t.tcl                  =
=======================================================

Program Information:
ESPResSo: 3.0.1
{ Compilation status { FFTW } { PARTIAL_PERIODIC } { ELECTROSTATICS } { 
MASS } { EXTERNAL_FORCES } { CONSTRAINTS } { EXCLUSIONS } { COMFORCE } { 
COMFIXED } { TABULATED } { LENNARD_JONES } { LENNARD_JONES_GENERIC } { 
MORSE } { BUCKINGHAM } { SOFT_SPHERE } { LJCOS } { LJCOS2 } { 
BOND_ANGLE_COSINE } { NPT } }
{ Debug status { MPI_CORE FORCE_CORE } }

Adress is not compiled in (change config.h).
     while executing
"adress set topo $topo_kind width [expr $ex_width*0.5] $hyb_width center 
x $ex_center wf $wf "
     (file "./samples/adress/Adress_t.tcl" line 65)

What can i do??I think ADRESS is compiled!!
Do i change */espresso-3.0.1/src/config.h* or 
*/espresso-3.0.1/myconfig-sample.h*????And what do i change???

Thanx
-------------- next part --------------
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------------------------------

Message: 2
Date: Tue, 06 Sep 2011 09:51:39 +0200
From: Olaf Lenz <address@hidden>
To: address@hidden
Subject: Re: [ESPResSo-users] ADRess trouble
Message-ID: <address@hidden>
Content-Type: text/plain; charset="iso-8859-15"

Hi!

Have a look at the User's Guide, chapter 3.4 "myconfig.h: Activating and
deactivating features".

Olaf

On 09/06/2011 09:55 AM, Nicola Fortunati wrote:

Hi Espresso users,

i want to install *ADRESS FEATURE* in my *ESPRESSO CODE*.
After *compile*, *make* and *make check* i tested Adress tcl script and
ESPRESSO returned this message:

address@hidden espresso-3.0.1]# ./Espresso ./samples/adress/Adress_t.tcl
0: Script directory: /home/nicolafortunati/Scrivania/espresso-3.0.1/scripts
*******************************************************
*                                                     *
*                    - ESPResSo -                     *
*                    ============                     *
*        A Parallel Molecular Dynamics Program        *
*                                                     *
* (c) 2010,2011                                       *
* The ESPResSo project                                *
*                                                     *
* (c) 2002,2003,2004,2005,2006,2007,2008,2009,2010    *
* Max-Planck-Institute for Polymer Research           *
* Mainz, Germany                                      *
*                                                     *
*******************************************************

ESPResSo 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.

ESPResSo 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/>.

 
=======================================================
=              Script:  Adress_t.tcl                  =
=======================================================
 
Program Information:
ESPResSo: 3.0.1
{ Compilation status { FFTW } { PARTIAL_PERIODIC } { ELECTROSTATICS } {
MASS } { EXTERNAL_FORCES } { CONSTRAINTS } { EXCLUSIONS } { COMFORCE } {
COMFIXED } { TABULATED } { LENNARD_JONES } { LENNARD_JONES_GENERIC } {
MORSE } { BUCKINGHAM } { SOFT_SPHERE } { LJCOS } { LJCOS2 } {
BOND_ANGLE_COSINE } { NPT } }
{ Debug status { MPI_CORE FORCE_CORE } }

Adress is not compiled in (change config.h).
    while executing
"adress set topo $topo_kind width [expr $ex_width*0.5] $hyb_width center
x $ex_center wf $wf "
    (file "./samples/adress/Adress_t.tcl" line 65)

What can i do??I think ADRESS is compiled!!
Do i change */espresso-3.0.1/src/config.h* or
*/espresso-3.0.1/myconfig-sample.h*????And what do i change???

Thanx


    

    Dear all,

    

    i have looked User's Guide, chapter 3.4 "myconfig.h: Activating
      and deactivating features", but i can't to compile with ADRESS
    feature and i don't understand why i can't do it.

    I want to use ADRESS to simulate proteins into CG solvent.

    My operations to install ADRESS are:
    
    
      
  •  have modified the file /espresso-3.0.1/src/myconfig-default.h:
        i have added the configuration header #define ADRESSO.
    • 
    

    #define PARTIAL_PERIODIC

        #define ELECTROSTATICS

        #define EXTERNAL_FORCES

        #define CONSTRAINTS

        #define MASS

        #define EXCLUSIONS

        #define COMFORCE

        #define COMFIXED

        #define NPT

        

        /* potentials */

        #define TABULATED

        #define LENNARD_JONES

        #define LENNARD_JONES_GENERIC

        #define MORSE

        #define LJCOS

        #define LJCOS2

        #define BUCKINGHAM

        #define SOFT_SPHERE

        #define BOND_ANGLE_COSINE

        

        #define MPI_CORE

        #define FORCE_CORE

        

        #define ADRESSO

        #define VIRTUAL_SITES_COM

      

    
    
      
  • I copied/espresso-3.0.1/src/myconfig-default.h  in /espresso-3.0.1/myconfig-default.h.
    • 
      
  • I used configure script:No problems.
    • 
    

    $ ./configure --without-mpi
        --with-myconfig=myconfig-default.h

        checking build system type... x86_64-unknown-linux-gnu

        checking host system type... x86_64-unknown-linux-gnu

        checking target system type... x86_64-unknown-linux-gnu

        checking for a BSD-compatible install... /usr/bin/install -c

        checking whether build environment is sane... yes

        checking for a thread-safe mkdir -p... /bin/mkdir -p

        checking for gawk... gawk

        checking whether make sets $(MAKE)... yes

        checking whether to enable maintainer-specific portions of
        Makefiles... no

        ****************************************************************

        *      Checking compiler characteristics and MPI support       *

        ****************************************************************

        checking for style of include used by make... GNU

        checking whether to compile using MPI... no

        checking for gcc... gcc

        checking whether the C compiler works... yes

        checking for C compiler default output file name... a.out

        checking for suffix of executables... 

        checking whether we are cross compiling... no

        checking for suffix of object files... o

        checking whether we are using the GNU C compiler... yes

        checking for gcc option to accept ISO C89... none needed

        checking dependency style of gcc... gcc3

        configure: WARNING: No MPI compiler found, will use fake
        implementation!

        checking whether the compiler accepts -O5... yes

        checking whether the compiler accepts -Wall... yes

        checking how to inline functions... static inline

        checking for gcc option to accept ISO C99... -std=gnu99

        checking for gcc -std=gnu99 option to accept ISO Standard C...
        (cached) -std=gnu99

        checking whether gcc -std=gnu99 and cc understand -c and -o
        together... yes

        checking for an ANSI C-conforming const... yes

        checking whether time.h and sys/time.h may both be included...
        yes

        ****************************************************************

        *                  Checking for programs                       *

        ****************************************************************

        checking for gawk... (cached) gawk

        checking for grep that handles long lines and -e... /bin/grep

        checking for egrep... /bin/grep -E

        checking for ranlib... ranlib

        checking whether ln -s works... yes

        checking for doxygen... /usr/bin/doxygen

        checking for dot... no

        checking for pdflatex... /usr/bin/pdflatex

        checking for makeindex... /usr/bin/makeindex

        checking for bibtex... /usr/bin/bibtex

        ****************************************************************

        *               Checking for standard headers                  *

        ****************************************************************

        checking how to run the C preprocessor... gcc -std=gnu99 -E

        checking for ANSI C header files... yes

        checking for sys/types.h... yes

        checking for sys/stat.h... yes

        checking for stdlib.h... yes

        checking for string.h... yes

        checking for memory.h... yes

        checking for strings.h... yes

        checking for inttypes.h... yes

        checking for stdint.h... yes

        checking for unistd.h... yes

        checking arpa/inet.h usability... yes

        checking arpa/inet.h presence... yes

        checking for arpa/inet.h... yes

        checking fcntl.h usability... yes

        checking fcntl.h presence... yes

        checking for fcntl.h... yes

        checking float.h usability... yes

        checking float.h presence... yes

        checking for float.h... yes

        checking for inttypes.h... (cached) yes

        checking limits.h usability... yes

        checking limits.h presence... yes

        checking for limits.h... yes

        checking netdb.h usability... yes

        checking netdb.h presence... yes

        checking for netdb.h... yes

        checking netinet/in.h usability... yes

        checking netinet/in.h presence... yes

        checking for netinet/in.h... yes

        checking stddef.h usability... yes

        checking stddef.h presence... yes

        checking for stddef.h... yes

        checking for stdlib.h... (cached) yes

        checking for string.h... (cached) yes

        checking for strings.h... (cached) yes

        checking sys/file.h usability... yes

        checking sys/file.h presence... yes

        checking for sys/file.h... yes

        checking sys/socket.h usability... yes

        checking sys/socket.h presence... yes

        checking for sys/socket.h... yes

        checking sys/time.h usability... yes

        checking sys/time.h presence... yes

        checking for sys/time.h... yes

        checking for unistd.h... (cached) yes

        ****************************************************************

        *               Checking for standard functions                *

        ****************************************************************

        checking for stdlib.h... (cached) yes

        checking for GNU libc compatible malloc... yes

        checking for working memcmp... yes

        checking for stdlib.h... (cached) yes

        checking for GNU libc compatible realloc... yes

        checking sys/select.h usability... yes

        checking sys/select.h presence... yes

        checking for sys/select.h... yes

        checking for sys/socket.h... (cached) yes

        checking types of arguments for select... int,fd_set *,struct
        timeval *

        checking for size_t... yes

        checking for working strtod... yes

        checking for atexit... yes

        checking for floor... no

        checking for getcwd... yes

        checking for gethostbyname... yes

        checking for memset... yes

        checking for pow... no

        checking for rint... no

        checking for select... yes

        checking for socket... yes

        checking for sqrt... no

        ****************************************************************

        *         Checking for required tools and libraries            *

        ****************************************************************

        checking for libtcl8.6... no

        checking for libtcl8.5... yes

        checking for tcl.h... yes

        checking whether to use FFTW... guess

        checking for library containing fftw_plan_many_dft... -lfftw3

        checking fftw3.h usability... yes

        checking fftw3.h presence... yes

        checking for fftw3.h... yes

        checking whether to use CUDA... no

        ****************************************************************

        *                   Other settings                             *

        ****************************************************************

        checking whether to use efence... no

        checking the name of the configuration header...
        myconfig-default.h

        checking the number of available CPUs... 2 

        ****************************************************************

        *                   Creating output files                      *

        ****************************************************************

        configure: creating ./config.status

        config.status: creating Makefile

        config.status: creating src/Makefile

        config.status: creating tools/Makefile

        config.status: creating scripts/Makefile

        config.status: creating testsuite/Makefile

        config.status: creating testsuite/configs/Makefile

        config.status: creating doc/Makefile

        config.status: creating doc/dg/Makefile

        config.status: creating doc/ug/Makefile

        config.status: creating doc/tutorials/Makefile

        config.status: creating doc/tutorials/tut2/Makefile

        config.status: creating doc/latexit.sh

        config.status: creating myconfig-sample.h

        config.status: creating testsuite/runtest.sh

        config.status: creating tools/es_mpiexec

        config.status: creating src/acconfig.h

        config.status: src/acconfig.h is unchanged

        config.status: executing depfiles commands

        ****************************************************************

        *                   Configuration summary                      *

        ****************************************************************

        platform detected    = x86_64-unknown-linux-gnu

        

        Compiler settings:

        ------------------

        compiler        = gcc -std=gnu99

        linker            = 

        c compiler flags    = -Wall -O5 

        c preprocessor flags    = 

        linker flags        = 

        libraries        = -lfftw3 -ltcl8.5  -lm

        using debug flags    = 

        using profiling flags    = 

        inline            = 

        

        Libraries:

        ----------

        Tcl version        = tcl8.5

        Tk version        = none

        FFTW             = yes

        efence            = no

        

        Other settings:

        ---------------

        local config header    = myconfig-default.h

        installation prefix    = /home/nicolafortunati/Espresso

        number of test tasks    = 2

        mympiexec               = 

        mpiexec                 = 

        pdflatex        = /usr/bin/pdflatex

        makeindex        = /usr/bin/makeindex

        bibtex            = /usr/bin/bibtex

        doxygen            = /usr/bin/doxygen

        dot            = 

        

        WARNING: MPI disabled or not supported! Parallelization turned
        off.

        CUDA disabled or not supported.

        

        

      
    
    
      
  • I used Makefile script:Problems!!!
    • 
    

    $ make

        Making all in src

        make[1]: Entering directory
        `/home/nicolafortunati/Scrivania/ADRESS/espresso-3.0.1/src'

        make  all-am

        make[2]: Entering directory
        `/home/nicolafortunati/Scrivania/ADRESS/espresso-3.0.1/src'

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -DBLOCKFILE_STDIO   -Wall
        -O5  -MT libespressobf_a-blockfile.o -MD -MP -MF
        .deps/libespressobf_a-blockfile.Tpo -c -o
        libespressobf_a-blockfile.o `test -f 'blockfile.c' || echo
        './'`blockfile.c

        mv -f .deps/libespressobf_a-blockfile.Tpo
        .deps/libespressobf_a-blockfile.Po

        rm -f libespressobf.a

        ar cru libespressobf.a libespressobf_a-blockfile.o 

        ranlib libespressobf.a

        config_files="\

          ../myconfig-default.h \

          ../myconfig-default.h"; \

        if test myconfig-default.h = myconfig.h; then \

          config_files="$config_files ../src/myconfig-default.h"; \

        fi; \

        for file in $config_files; do \

          if test -e $file; then \

            myconfig_found=1; \

            if test -e myconfig-final.h; then \

              cmp -s $file myconfig-final.h || cp $file
        myconfig-final.h; \

            else \

               cp $file myconfig-final.h; \

            fi; \

            break; \

          fi; \

        done; \

        if test ! $myconfig_found; then \

          echo "ERROR: Couldn't find myconfig-default.h anywhere"; \

          exit 1; \

        fi

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        config.o -MD -MP -MF .deps/config.Tpo -c -o config.o config.c

        mv -f .deps/config.Tpo .deps/config.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        initialize.o -MD -MP -MF .deps/initialize.Tpo -c -o initialize.o
        initialize.c

        mv -f .deps/initialize.Tpo .deps/initialize.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        global.o -MD -MP -MF .deps/global.Tpo -c -o global.o global.c

        mv -f .deps/global.Tpo .deps/global.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        communication.o -MD -MP -MF .deps/communication.Tpo -c -o
        communication.o communication.c

        mv -f .deps/communication.Tpo .deps/communication.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        binary_file.o -MD -MP -MF .deps/binary_file.Tpo -c -o
        binary_file.o binary_file.c

        mv -f .deps/binary_file.Tpo .deps/binary_file.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        interaction_data.o -MD -MP -MF .deps/interaction_data.Tpo -c -o
        interaction_data.o interaction_data.c

        mv -f .deps/interaction_data.Tpo .deps/interaction_data.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        verlet.o -MD -MP -MF .deps/verlet.Tpo -c -o verlet.o verlet.c

        mv -f .deps/verlet.Tpo .deps/verlet.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        grid.o -MD -MP -MF .deps/grid.Tpo -c -o grid.o grid.c

        mv -f .deps/grid.Tpo .deps/grid.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        integrate.o -MD -MP -MF .deps/integrate.Tpo -c -o integrate.o
        integrate.c

        mv -f .deps/integrate.Tpo .deps/integrate.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        cells.o -MD -MP -MF .deps/cells.Tpo -c -o cells.o cells.c

        mv -f .deps/cells.Tpo .deps/cells.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        ghosts.o -MD -MP -MF .deps/ghosts.Tpo -c -o ghosts.o ghosts.c

        mv -f .deps/ghosts.Tpo .deps/ghosts.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        forces.o -MD -MP -MF .deps/forces.Tpo -c -o forces.o forces.c

        mv -f .deps/forces.Tpo .deps/forces.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        rotation.o -MD -MP -MF .deps/rotation.Tpo -c -o rotation.o
        rotation.c

        mv -f .deps/rotation.Tpo .deps/rotation.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        debug.o -MD -MP -MF .deps/debug.Tpo -c -o debug.o debug.c

        mv -f .deps/debug.Tpo .deps/debug.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        particle_data.o -MD -MP -MF .deps/particle_data.Tpo -c -o
        particle_data.o particle_data.c

        mv -f .deps/particle_data.Tpo .deps/particle_data.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        thermostat.o -MD -MP -MF .deps/thermostat.Tpo -c -o thermostat.o
        thermostat.c

        mv -f .deps/thermostat.Tpo .deps/thermostat.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        dpd.o -MD -MP -MF .deps/dpd.Tpo -c -o dpd.o dpd.c

        mv -f .deps/dpd.Tpo .deps/dpd.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        statistics.o -MD -MP -MF .deps/statistics.Tpo -c -o statistics.o
        statistics.c

        statistics.c: In function ‘tclcommand_analyze’:

        statistics.c:3778:3: warning: implicit declaration of function
        ‘tclcommand_analyze_parse_and_print_dipmom_mol’

        mv -f .deps/statistics.Tpo .deps/statistics.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        statistics_chain.o -MD -MP -MF .deps/statistics_chain.Tpo -c -o
        statistics_chain.o statistics_chain.c

        mv -f .deps/statistics_chain.Tpo .deps/statistics_chain.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        energy.o -MD -MP -MF .deps/energy.Tpo -c -o energy.o energy.c

        mv -f .deps/energy.Tpo .deps/energy.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        pressure.o -MD -MP -MF .deps/pressure.Tpo -c -o pressure.o
        pressure.c

        mv -f .deps/pressure.Tpo .deps/pressure.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        vmdsock.o -MD -MP -MF .deps/vmdsock.Tpo -c -o vmdsock.o
        vmdsock.c

        mv -f .deps/vmdsock.Tpo .deps/vmdsock.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        imd.o -MD -MP -MF .deps/imd.Tpo -c -o imd.o imd.c

        mv -f .deps/imd.Tpo .deps/imd.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        iccp3m.o -MD -MP -MF .deps/iccp3m.Tpo -c -o iccp3m.o iccp3m.c

        mv -f .deps/iccp3m.Tpo .deps/iccp3m.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        p3m-common.o -MD -MP -MF .deps/p3m-common.Tpo -c -o p3m-common.o
        p3m-common.c

        mv -f .deps/p3m-common.Tpo .deps/p3m-common.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        p3m.o -MD -MP -MF .deps/p3m.Tpo -c -o p3m.o p3m.c

        mv -f .deps/p3m.Tpo .deps/p3m.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        p3m-magnetostatics.o -MD -MP -MF .deps/p3m-magnetostatics.Tpo -c
        -o p3m-magnetostatics.o p3m-magnetostatics.c

        mv -f .deps/p3m-magnetostatics.Tpo .deps/p3m-magnetostatics.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        magnetic_non_p3m_methods.o -MD -MP -MF
        .deps/magnetic_non_p3m_methods.Tpo -c -o
        magnetic_non_p3m_methods.o magnetic_non_p3m_methods.c

        mv -f .deps/magnetic_non_p3m_methods.Tpo
        .deps/magnetic_non_p3m_methods.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        ewald.o -MD -MP -MF .deps/ewald.Tpo -c -o ewald.o ewald.c

        mv -f .deps/ewald.Tpo .deps/ewald.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        fft.o -MD -MP -MF .deps/fft.Tpo -c -o fft.o fft.c

        mv -f .deps/fft.Tpo .deps/fft.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        random.o -MD -MP -MF .deps/random.Tpo -c -o random.o random.c

        mv -f .deps/random.Tpo .deps/random.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        blockfile.o -MD -MP -MF .deps/blockfile.Tpo -c -o blockfile.o
        blockfile.c

        mv -f .deps/blockfile.Tpo .deps/blockfile.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        blockfile_tcl.o -MD -MP -MF .deps/blockfile_tcl.Tpo -c -o
        blockfile_tcl.o blockfile_tcl.c

        mv -f .deps/blockfile_tcl.Tpo .deps/blockfile_tcl.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        polymer.o -MD -MP -MF .deps/polymer.Tpo -c -o polymer.o
        polymer.c

        mv -f .deps/polymer.Tpo .deps/polymer.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        specfunc.o -MD -MP -MF .deps/specfunc.Tpo -c -o specfunc.o
        specfunc.c

        mv -f .deps/specfunc.Tpo .deps/specfunc.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        tuning.o -MD -MP -MF .deps/tuning.Tpo -c -o tuning.o tuning.c

        mv -f .deps/tuning.Tpo .deps/tuning.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        uwerr.o -MD -MP -MF .deps/uwerr.Tpo -c -o uwerr.o uwerr.c

        mv -f .deps/uwerr.Tpo .deps/uwerr.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        parser.o -MD -MP -MF .deps/parser.Tpo -c -o parser.o parser.c

        mv -f .deps/parser.Tpo .deps/parser.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        domain_decomposition.o -MD -MP -MF
        .deps/domain_decomposition.Tpo -c -o domain_decomposition.o
        domain_decomposition.c

        mv -f .deps/domain_decomposition.Tpo
        .deps/domain_decomposition.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        nsquare.o -MD -MP -MF .deps/nsquare.Tpo -c -o nsquare.o
        nsquare.c

        mv -f .deps/nsquare.Tpo .deps/nsquare.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        layered.o -MD -MP -MF .deps/layered.Tpo -c -o layered.o
        layered.c

        mv -f .deps/layered.Tpo .deps/layered.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        mmm-common.o -MD -MP -MF .deps/mmm-common.Tpo -c -o mmm-common.o
        mmm-common.c

        mv -f .deps/mmm-common.Tpo .deps/mmm-common.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        mmm1d.o -MD -MP -MF .deps/mmm1d.Tpo -c -o mmm1d.o mmm1d.c

        mv -f .deps/mmm1d.Tpo .deps/mmm1d.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        mmm2d.o -MD -MP -MF .deps/mmm2d.Tpo -c -o mmm2d.o mmm2d.c

        mv -f .deps/mmm2d.Tpo .deps/mmm2d.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        modes.o -MD -MP -MF .deps/modes.Tpo -c -o modes.o modes.c

        mv -f .deps/modes.Tpo .deps/modes.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        topology.o -MD -MP -MF .deps/topology.Tpo -c -o topology.o
        topology.c

        mv -f .deps/topology.Tpo .deps/topology.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        nemd.o -MD -MP -MF .deps/nemd.Tpo -c -o nemd.o nemd.c

        mv -f .deps/nemd.Tpo .deps/nemd.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        statistics_cluster.o -MD -MP -MF .deps/statistics_cluster.Tpo -c
        -o statistics_cluster.o statistics_cluster.c

        mv -f .deps/statistics_cluster.Tpo .deps/statistics_cluster.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        elc.o -MD -MP -MF .deps/elc.Tpo -c -o elc.o elc.c

        mv -f .deps/elc.Tpo .deps/elc.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        mdlc_correction.o -MD -MP -MF .deps/mdlc_correction.Tpo -c -o
        mdlc_correction.o mdlc_correction.c

        mv -f .deps/mdlc_correction.Tpo .deps/mdlc_correction.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        statistics_molecule.o -MD -MP -MF .deps/statistics_molecule.Tpo
        -c -o statistics_molecule.o statistics_molecule.c

        mv -f .deps/statistics_molecule.Tpo .deps/statistics_molecule.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        errorhandling.o -MD -MP -MF .deps/errorhandling.Tpo -c -o
        errorhandling.o errorhandling.c

        mv -f .deps/errorhandling.Tpo .deps/errorhandling.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        constraint.o -MD -MP -MF .deps/constraint.Tpo -c -o constraint.o
        constraint.c

        mv -f .deps/constraint.Tpo .deps/constraint.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        maggs.o -MD -MP -MF .deps/maggs.Tpo -c -o maggs.o maggs.c

        mv -f .deps/maggs.Tpo .deps/maggs.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        rattle.o -MD -MP -MF .deps/rattle.Tpo -c -o rattle.o rattle.c

        mv -f .deps/rattle.Tpo .deps/rattle.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        molforces.o -MD -MP -MF .deps/molforces.Tpo -c -o molforces.o
        molforces.c

        mv -f .deps/molforces.Tpo .deps/molforces.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        virtual_sites.o -MD -MP -MF .deps/virtual_sites.Tpo -c -o
        virtual_sites.o virtual_sites.c

        mv -f .deps/virtual_sites.Tpo .deps/virtual_sites.Po

        gcc -std=gnu99 -DHAVE_CONFIG_H -I.  -I./mpifake   -Wall -O5  -MT
        virtual_sites_com.o -MD -MP -MF .deps/virtual_sites_com.Tpo -c
        -o virtual_sites_com.o virtual_sites_com.c

        In file included from virtual_sites_com.c:20:0:

        virtual_sites_com.h:31:39: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.h:32:39: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.h:41:10: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
        or ‘__attribute__’ before ‘*’ token

        virtual_sites_com.h:45:30: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.h:48:38: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:25:28: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:26:28: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:27:31: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:28:38: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:30:39: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:42:39: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c: In function ‘distribute_mol_force’:

        virtual_sites_com.c:56:3: error: ‘Particle’ undeclared (first
        use in this function)

        virtual_sites_com.c:56:3: note: each undeclared identifier is
        reported only once for each function it appears in

        virtual_sites_com.c:56:13: error: ‘p’ undeclared (first use in
        this function)

        virtual_sites_com.c:58:3: error: ‘Cell’ undeclared (first use in
        this function)

        virtual_sites_com.c:58:9: error: ‘cell’ undeclared (first use in
        this function)

        virtual_sites_com.c:59:19: error: ‘local_cells’ undeclared
        (first use in this function)

        virtual_sites_com.c:64:7: warning: implicit declaration of
        function ‘ifParticleIsVirtual’

        virtual_sites_com.c:65:10: warning: implicit declaration of
        function ‘sqrlen’

        virtual_sites_com.c:66:13: warning: implicit declaration of
        function ‘put_mol_force_on_parts’

        virtual_sites_com.c: At top level:

        virtual_sites_com.c:73:28: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:116:28: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:161:31: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:195:38: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:251:10: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
        or ‘__attribute__’ before ‘*’ token

        virtual_sites_com.c:278:30: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c:311:10: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
        or ‘__attribute__’ before ‘*’ token

        virtual_sites_com.c: In function
        ‘tclcommand_analyze_parse_and_print_pressure_mol’:

        virtual_sites_com.c:326:4: warning: implicit declaration of
        function ‘updatePartCfg’

        virtual_sites_com.c:326:18: error: ‘WITHOUT_BONDS’ undeclared
        (first use in this function)

        virtual_sites_com.c:327:4: warning: implicit declaration of
        function ‘sortPartCfg’

        virtual_sites_com.c:328:7: warning: implicit declaration of
        function ‘runtime_error’

        virtual_sites_com.c:328:22: warning: initialization makes
        pointer from integer without a cast

        virtual_sites_com.c:329:7: warning: implicit declaration of
        function ‘ERROR_SPRINTF’

        virtual_sites_com.c:338:4: warning: implicit declaration of
        function ‘ARG0_IS_I’

        virtual_sites_com.c:343:4: warning: implicit declaration of
        function ‘ARG1_IS_I’

        virtual_sites_com.c:350:8: error: ‘n_molecules’ undeclared
        (first use in this function)

        virtual_sites_com.c: In function
        ‘tclcommand_analyze_parse_and_print_energy_kinetic_mol’:

        virtual_sites_com.c:370:18: error: ‘WITHOUT_BONDS’ undeclared
        (first use in this function)

        virtual_sites_com.c:372:22: warning: initialization makes
        pointer from integer without a cast

        virtual_sites_com.c:389:8: error: ‘n_molecules’ undeclared
        (first use in this function)

        virtual_sites_com.c: In function ‘calc_pressure_mol’:

        virtual_sites_com.c:411:14: error: ‘n_molecules’ undeclared
        (first use in this function)

        virtual_sites_com.c:412:9: error: ‘topology’ undeclared (first
        use in this function)

        virtual_sites_com.c: In function
        ‘tclcommand_analyze_parse_and_print_dipmom_mol’:

        virtual_sites_com.c:447:18: error: ‘WITHOUT_BONDS’ undeclared
        (first use in this function)

        virtual_sites_com.c:449:22: warning: initialization makes
        pointer from integer without a cast

        virtual_sites_com.c:453:8: error: ‘n_molecules’ undeclared
        (first use in this function)

        virtual_sites_com.c:469:4: warning: implicit declaration of
        function ‘ARG0_IS_S’

        virtual_sites_com.c: In function ‘calc_force_between_mol’:

        virtual_sites_com.c:503:3: error: ‘Particle’ undeclared (first
        use in this function)

        virtual_sites_com.c:503:13: error: ‘p1’ undeclared (first use in
        this function)

        virtual_sites_com.c:503:17: error: ‘p2’ undeclared (first use in
        this function)

        virtual_sites_com.c:503:15: warning: left-hand operand of comma
        _expression_ has no effect

        virtual_sites_com.c:511:14: error: ‘topology’ undeclared (first
        use in this function)

        virtual_sites_com.c:512:9: error: ‘partCfg’ undeclared (first
        use in this function)

        virtual_sites_com.c:516:7: warning: implicit declaration of
        function ‘get_mi_vector’

        virtual_sites_com.c:518:7: warning: implicit declaration of
        function ‘sqrt’

        virtual_sites_com.c:518:12: warning: incompatible implicit
        declaration of built-in function ‘sqrt’

        virtual_sites_com.c:523:7: warning: implicit declaration of
        function ‘do_nonbonded’

        virtual_sites_com.c:526:4: warning: implicit declaration of
        function ‘calc_non_bonded_pair_force_from_partcfg_simple’

        virtual_sites_com.c:527:4: warning: implicit declaration of
        function ‘adress_non_bonded_force_weight’

        virtual_sites_com.c: In function ‘calc_energy_kinetic_mol’:

        virtual_sites_com.c:546:4: error: ‘Particle’ undeclared (first
        use in this function)

        virtual_sites_com.c:546:14: error: ‘p_com’ undeclared (first use
        in this function)

        virtual_sites_com.c:547:15: error: ‘n_molecules’ undeclared
        (first use in this function)

        virtual_sites_com.c:548:11: error: ‘topology’ undeclared (first
        use in this function)

        virtual_sites_com.c:549:10: warning: implicit declaration of
        function ‘get_mol_com_particle_from_molid_cfg’

        virtual_sites_com.c:558:10: warning: implicit declaration of
        function ‘PMASS’

        virtual_sites_com.c:561:15: error: ‘time_step’ undeclared (first
        use in this function)

        virtual_sites_com.c: In function
        ‘calc_absolute_dipolmoment_mol’:

        virtual_sites_com.c:570:15: error: ‘n_molecules’ undeclared
        (first use in this function)

        virtual_sites_com.c:571:11: error: ‘topology’ undeclared (first
        use in this function)

        virtual_sites_com.c: In function ‘calc_total_dipolmoment_mol’:

        virtual_sites_com.c:590:15: error: ‘n_molecules’ undeclared
        (first use in this function)

        virtual_sites_com.c:591:11: error: ‘topology’ undeclared (first
        use in this function)

        virtual_sites_com.c: In function ‘calc_dipole_of_molecule’:

        virtual_sites_com.c:602:4: error: ‘Particle’ undeclared (first
        use in this function)

        virtual_sites_com.c:602:14: error: ‘p’ undeclared (first use in
        this function)

        virtual_sites_com.c:602:17: error: ‘p_first’ undeclared (first
        use in this function)

        virtual_sites_com.c:602:15: warning: left-hand operand of comma
        _expression_ has no effect

        virtual_sites_com.c:605:15: error: ‘topology’ undeclared (first
        use in this function)

        virtual_sites_com.c:606:10: error: ‘partCfg’ undeclared (first
        use in this function)

        virtual_sites_com.c: At top level:

        virtual_sites_com.c:623:10: error: expected ‘=’, ‘,’, ‘;’, ‘asm’
        or ‘__attribute__’ before ‘*’ token

        virtual_sites_com.c:638:38: error: expected ‘)’ before ‘*’ token

        virtual_sites_com.c: In function
        ‘get_mol_dist_vector_from_molid_cfg’:

        virtual_sites_com.c:649:4: error: ‘Particle’ undeclared (first
        use in this function)

        virtual_sites_com.c:649:14: error: ‘p1_com’ undeclared (first
        use in this function)

        virtual_sites_com.c:649:22: error: ‘p2_com’ undeclared (first
        use in this function)

        virtual_sites_com.c:649:20: warning: left-hand operand of comma
        _expression_ has no effect

        virtual_sites_com.c: In function
        ‘tclcommand_analyze_parse_and_print_check_mol’:

        virtual_sites_com.c:671:4: error: ‘Particle’ undeclared (first
        use in this function)

        virtual_sites_com.c:671:13: error: expected ‘;’ before ‘p’

        virtual_sites_com.c:672:18: error: ‘WITHOUT_BONDS’ undeclared
        (first use in this function)

        virtual_sites_com.c:673:15: error: ‘n_total_particles’
        undeclared (first use in this function)

        virtual_sites_com.c:674:33: error: ‘partCfg’ undeclared (first
        use in this function)

        virtual_sites_com.c:675:7: warning: implicit declaration of
        function ‘get_particle_data’

        virtual_sites_com.c:675:28: error: ‘p’ undeclared (first use in
        this function)

        virtual_sites_com.c:677:7: warning: implicit declaration of
        function ‘unfold_position’

        virtual_sites_com.c:678:7: warning: implicit declaration of
        function ‘distance’

        make[2]: *** [virtual_sites_com.o] Errore 1

        make[2]: Leaving directory
        `/home/nicolafortunati/Scrivania/ADRESS/espresso-3.0.1/src'

        make[1]: *** [all] Errore 2

        make[1]: Leaving directory
        `/home/nicolafortunati/Scrivania/ADRESS/espresso-3.0.1/src'

        make: *** [all-recursive] Errore 1

        

            Do i have to modify and to use /espresso-3.0.1/myconfig-sample.h 
            with configure script???? I tried to, but at the end
            of compiling that file was cleared.

            Could you help me???

            

            Thank you very much.
  















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