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ÈçºÎѧϰlammps£¿Äã¿ÉÒ԰ѱ¾½Ì³Ìµ±×öÒ»¸ö¿ªÊ¼¡£lammpsµÄÊÖ²áÖÐÏêϸ½éÉÜÁËÈí¼þµÄ¸÷¸ö·½Ãæ¡£Ò»¶¨ÒªºÃºÃÔĶÁÊֲᡣÊÖ²áµÄÇ°ËÄÕÂÒªÈÏÕæÔĶÁ¡£¾³£Ê¹ÓõÄÃüÁîÒ²Òª×ÐϸÔĶÁ¡£µ±ÄãҪʵÏÖijÖÖ¹¦ÄܵÄʱºò¾Í°ÑÊÖ²á´ò¿ª¿´¿´ÃüÁî¡£×ÐϸÔĶÁѧϰlammps¹Ù·½ÊÖ²áÊdzÉΪlammps¸ßÊֵıؾ֮·£¬ÔĶÁѧϰһ±¾·Ö×Ó¶¯Á¦Ñ§Ä£Äâ¾µä½Ì²ÄÊÇÔö¼ÓÐÞΪµÄ¹Ø¼ü¡£Ï£Íû±¾½Ì³ÌÄ̻ܽáÄãlammpsµÄ»ù±¾ÕÐʽ¡£×£ÄãºÃÔË£¡
lammps¹ÙÍøÍƼöÁ˼¸±¾·Ö×Ó¶¯Á¦Ñ§Ä£Äâ½Ì²Ä£º
books about molecular dynamics generally or lammps specifically
note that these are not endorsements of particular books. we simply want to make the lammps user community aware of them as potentially useful resources.
general md books:
allen & tildesley - computer simulation of liquids
frenkel & smit - understanding molecular simulation: from algorithms to application
griebel, knapek, zumbusch - numerical simulation in molecular dynamics: numerics, algorithms, parallelization, applications
tuckerman - statistical mechanics: theory and molecular simulation
books about lammps specifically:
mubin & li - extending and modifying lammps (see below)
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path=$path:<·¾¶Ãû>£¬°´esc¼üÍ˳ö±à¼Ä£Ê½£¬ÊäÈë:wqºó»Ø³µ£¬ÕâÑù¾Í±£´æºÃÁ˸ղŵı༣¬²¢Í˳öÁË.bashrcÎļþ»Øµ½ÁËÖնˡ£ÔÚÖÕ¶ËÊäÈësource ~/.bashrc¾Í¿ÉÒÔÊǸղŵIJÙ×÷·¢Éú×÷Óá£sudoÊÇÁÙʱȡµÃrootȨÏÞÃüÁµ±ÄãÒªÔÚϵͳĿ¼ÖÐÌí¼Ó»òÐÞ¸ÄÎļþµÄʱºò¾ÍÐèÒª°Ñsudo¼Óµ½Ö´ÐÐÃüÁîÇ°Ã棬Èçsudo cp ./lmp /usr/bin¾ÍÊǰѵ±Ç°Ä¿Â¼ÏµÄlmpÎļþ¿½±´µ½ÏµÍ³Ä¿Â¼/usr/binÖС£´øÓÐsudoµÄÃüÁî»Ø³µÖ´ÐкóÐèÒªÊäÈëÓû§ÃÜÂ룬µ±ÄãÔÚÊäÈëÃÜÂëµÄʱºòÖÕ¶ËÉϲ»»áÏÔʾÃÜÂ룬µ«ÊÇȷʵÊÇÊä½øÈ¥ÁË£¬ÊäÍê»Ø³µÈç¹ûÃÜÂëÕýÈ·¾Í¿ªÊ¼Ö´ÐÐÃüÁîÁË¡£ÆäËûÃüÁî¿ÉÒÔ°Ù¶ÈÄܹ»ÕÒµ½´óÁ¿×ÊÁÏ¡£µ±ÄãÔÚʹÓÃlinuxϵͳʱÐèÒªÎÊÒ»¸öÎÊÌ⣬Äã¾Í°Ù¶È£¬Ò»¶¨ÄÜÕÒµ½´ð°¸¡£
3. lammps½éÉܺͲ¢Ðа氲װ£¨linux°æ£©
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sudo apt-get update
sudo apt-get install build-essential
sudo apt-get install vim
µÚ¶þ²½ÊäÈëÖ´ÐÐ
mkdir /home/me/software
mkdir /home/me/software/mpich
mkdir /home/me/software/fftw
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tar -xvf <mpichѹËõÎļþµÄÃû³Æ>
tar -xvf <fftwѹËõÎļþµÄÃû³Æ>
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make
make install
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./configure -prefix=/home/me/software/fftw
make
make install
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vim ~/.bashrc
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path=$path:/home/me/software/mpich/bin
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source ~/.bashrc
which mpirun
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cd /home/me/software/½âѹ³öÀ´lammpsÎļþ¼ÐÃû³Æ/src
µÚ¾Å²½´ò¿ªÄ¿Â¼/home/me/software/½âѹ³öÀ´lammpsÎļþ¼ÐÃû³Æ/src/make/optionsϵÄmakefile.g++_mpichÎļþ¡£ÔÚÎļþÒÔÏÂλÖÃÐÞ¸ÄΪ
mpi_inc = -dmpich_skip_mpicxx -dompi_skip_mpicxx=1 -i/home/me/software/mpich/include
mpi_path = -l/home/me/software/mpich/lib
mpi_lib =
fft_inc = -i/home/me/software/fftw/include
fft_path = -l/home/me/software/fftw/lib
fft_lib =
±£´æÍ˳ö¡£
µÚÊ®²½ÔÚÖÕ¶ËÒÀ´ÎÖ´ÐÐ
make yes-molecule
make yes-kspace
make yes-rigid
make yes-manybody
make g++_mpich
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mpirun -np <²¢ÐкËÊý> ./lmp_g++_mpich -in <inÎļþÃû×Ö>
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freud = analysis library for post-processing md and mc data
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molecular builders
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intermol a conversion tool for molecular dynamics simulations
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automated topology builder (atb) and repository - molecular topology building blocks for organic molecules
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data sites
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jarvis database for md potential calculations on dft geometries
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orsi group at queen mary university of london
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