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From: | Nicola Fortunati |
Subject: | Re: [ESPResSo-users] Espressomd-users Digest, Vol 11, Issue 3 |
Date: | Tue, 27 Sep 2011 12:16:14 +0200 |
User-agent: | Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.22) Gecko/20110906 Fedora/3.1.14-1.fc14 Thunderbird/3.1.14 |
Il 06/09/2011 18:00, address@hidden ha scritto:
Dear all,Send Espressomd-users mailing list submissions to address@hidden To subscribe or unsubscribe via the World Wide Web, visit https://lists.nongnu.org/mailman/listinfo/espressomd-users or, via email, send a message with subject or body 'help' to address@hidden You can reach the person managing the list at address@hidden When replying, please edit your Subject line so it is more specific than "Re: Contents of Espressomd-users digest..." 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 -------------- An HTML attachment was scrubbed... URL: </archive/html/espressomd-users/attachments/20110906/0563b520/attachment.html> ------------------------------ 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 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:
#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
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.
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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