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USPEX能和Abinit interfece吗？
rt，想知道有没有预测晶体的软件可以和Abinit interfece的吗？
谢谢 版大 我看最新的manual有和abinit接口的打算。现在联系了吉大马老师的Cal也是不支持abinit。但这个接口应该就是在输入文件格式上的差别吧。
原来abinit有这个弊端，我说这么好的开源，更新也够快，怎么不支持呢。fzx圣诞快乐。
多谢指导。
:shuai: 这话应该早点看到……上阵子用Abinit试试弛豫，结果用PWscf做半个小时就出来的结构，用Abinit折腾了半天多……那结果是往死里收敛慢啊……
刚下好pwscf- - 一直都是abinit算的结构- -。 话说看到你那个XcryDen的帖子了，也正准备试一下-
呵呵 终于明白了！看来得慎用abinit……
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关注：1)对缺乏实验数据对比的、有争议的体系，有必要采用不同的预测方法预测，对比结果2）USPEX工作流程& 1. 参数准备：建立需预测结构目录，拷贝USPEX脚步进入该目录，在USPEX文件夹下 (1) 进入Specific/ & 设定INCAR1-5 (2) &进入USPEX目录，编辑：INPUT，设定体系组成，包含的分子数(如6 18 for M6H18)，体积(与M6H18对应的体积)，键长(参考汉典元素周期表中的共价键)，化合价(参考汉典元素周期表中的氧化态)等参数，无需特别指明VASP路径，程序会通过locate.m脚步定位可执行的VASP程序 (3) &进入USPEX/seeds/下，输入初始猜测的POSCAR，并命名为POSCARS，cp POSCARS seed注意：各文件夹下的可执行文件，应chmod +x 变成实际可执行的文件&&2. 提交： &matlab &USPEX.m& log & /opt/matlab2013/bin/matlab &&USPEX.m& log &或为保证程序周期性执行，修改并执行下述脚本，通过该脚本提交， &如，nohup ./run-uspex.sh，其中run-uspex.sh内容如下： cat &uspex_Sc-H #!/bin/shdo & & & &date & log & & & &/opt/matlab2013/bin/matlab && USPEX.m &&log & & & &sleep 60 &【估计每个优化任务运行时间，可通过延长sleep时间如600s，来延缓队列中提交的任务数量的增加速度】done&3. 看结果：进入results文件夹/ &vi goodstructures & &找到对应的低焓结构 &goodstructue_POSCAR4. 重新提交及杀掉任务（1） 每次重新提交，最好：rm -rf results* & &、./clean_tough（清除CalcFold*文件夹） & 、cp Seeds/seed Seeds/POSCARS（2） 改变VASP优化计算用CPU核的数目，需同时修改INPUT.TXT、submitJob_local.m、及Submission\submitJob_local.m下的CPU数目（3）如需 杀掉命令，则 ps aux | &grep uspexyexq & & 2 &0.0 12 pts/1 & &S & &04:51 & 0:00 /bin/sh ./uspex_Sc-Hyexq & & 3 &0.0 103244 & 876 pts/8 & &S+ & 05:15 & 0:00 grep uspexkill 23255对于在队列中已产生的大量任务，可通过脚本清除：cat del-uspex.sh #!/bin/shfor((i=50747;i&50767;i++))do & qdel $idone% i为Job ID.5. & 探索：1） matlab &USPEX.m& log & & 产生结构后，自动生成 提交 结构优化任务的vasp的脚本 & & vi results1/OUTPUT.txt ...... &* &There are &5 local relaxation steps for each individual structures *Step &Abinitio Code & & & & & & & & &Execute Command & & & & & &K-resolution &1 & & &VASP & & & & & & & & & & & & & & & & & & & vasp & & & & 0.160 &2 & & &VASP & & & & & & & & & & & & & & & & & & & vasp & & & & 0.120 &3 & & &VASP & & & & & & & & & & & & & & & & & & & vasp & & & & 0.100 &4 & & &VASP & & & & & & & & & & & & & & & & & & & vasp & & & & 0.080 &5 & & &VASP & & & & & & & & & & & & & & & & & & & vasp & & & & 0.060The script for job submission is prepared seperately in Submission/*_local.m & 5 parallel calculations are performed simutaneously2）解读 &Submission/*_local.m & &function doneOr = checkStatus_local(jobID)%--------------------------------------------------------------------%This routine is to check if the submitted job is done or not%One needs to do a little edit based on your own case.%1 & : whichCluster (0: no-job-script, 1: local submission, 2: remote submission)【在INPUT.TXT文件中已经指定】%--------------------------------------------------------------------%Step1: the command to check job by ID.
& &[a,b] = unix(['qstat ' jobID ''])%Step2: to find the keywords from screen message to determine if the job is done%Below is just a sample:%-------------------------------------------------------------------------------%Job id & & & & & & & & & &Name & & & & & & User & & & & & &Time Use S Queue%------------------------- ---------------- --------------- -------- - -----%2455453.nano & & & & & & &USPEX & & & & & &qzhu & & & & & &02:28:42 R cfn_gen04 %-------------------------------------------------------------------------------%If the job is still running, it will show as above.%If there is no key words like 'R/Q Cfn_gen04', it indicates the job is done. & &if isempty(findstr(b,'R low')) & isempty(findstr(b,'Q low'))
& & & doneOr = 1 & & & unix('rm USPEX*'); & &% to remove the log file & &else & & & doneOr = 0; & &endfunction jobNumber = submitJob_local()%-------------------------------------------------------------%This routine is to check if the submitted job is done or not%One needs to do a little edit based on your own case.1 & : whichCluster (default 0, 1: local submission, 2: remote submission)%-------------------------------------------------------------%Step 1: to prepare the job script which is required by your supercomputerfp = fopen('run.sh', 'w'); & &fprintf(fp, '#!/bin/sh\n');fprintf(fp, '#PBS -l nodes=1:ppn=6,walltime=2:00:00\n');fprintf(fp, '#PBS -N USPEX\n');fprintf(fp, '#PBS -j oe\n');%fprintf(fp, '#PBS -V \n');fprintf(fp, '#PBS -q dell\n'); &【自己服务器上的队列名称】%fprintf(fp, '#PBS -V \n');fprintf(fp, '#PBS -S /bin/bash\n');fprintf(fp, 'cd $PBS_O_WORKDIR\n');fprintf(fp,'mpirun &-np 8 vasp && vasp.out\n');fclose(fp);%Step 2: to submit the job with the command like qsub, bsub, llsubmit, .etc.%It will output some message on the screen like '2350873.nano.cfn.bnl.local'[a,b]=unix(['qsub run.sh'])%Step 3: to get the jobID from the screen messageend_marker = findstr(b,'.');jobNumber = b(1:end_marker(1)-1); &3） 解读：USPEX.m文件 cat & USPEX.m tryunix('chmod +x getStuff');unix('chmod +x getFromTo');unix('chmod +x FunctionFolder/USPEX/getStuff');unix('chmod +x FunctionFolder/USPEX/getFromTo');unix('chmod +x Specific/getStuff');unix('chmod +x Specific/getFromTo'); unix('chmod +x FunctionFolder/spacegroup_init/random_2d'); unix('chmod +x FunctionFolder/spacegroup_init/random_cell'); unix('chmod +x FunctionFolder/spacegroup_init/random_cell_mol'); unix('chmod +x FunctionFolder/spacegroup_stokes/findsym_new');catchend[nothing, whichCode] = unix(['./getStuff INPUT.txt calculationMethod 1']);if isempty(whichCode)whichCode = 'USPEX'; elsewhichCode(end) = [];endif strcmpi(whichCode, 'USPEX')ev_alg();elseif strcmpi(whichCode, 'VCNEB')vcNEB();elseif strcmpi(whichCode, 'META')metasoft();end4） &解读./getStuff#!/usr/bin/perl$file & =$string =$column =unless(defined($column)) { & & & &print &usage : &file& &string& &column&\n&; & & & &}open(FILE, $file) or die &Can't open $file : $!\n&;while(&FILE&) { & & & &if(/$string/) { & & & &@a = split /\s+/; & & & & & & & &print $a[$column-1] . &\n&; & & & &}}5）解读INPUT.txt PARAMETERS EVOLUTIONARY ALGORITHM************************************************************************************* & & &TYPE OF RUN AND SYSTEM & & & & & &*************************************************************************************USPEX : calculationMethod (USPEX, VCNEB, META)300 & : calculationType (dimension: 0-3; molecule: 0/1; varcomp: 0/1) &【变胞取1，如取301后，接下来如何处理？】1 & & : optType (1=enthalpy, 2=volume, 3=hardness, 4=struc_order, 5=aver_dist)%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% What symmetry(s) have to be satisfied by the randomly created structures% symmetries2-230% endSymmetries% numbers of specices (ions/molecules/blocks) of each type% numSpecices6 18% EndNumSpecices%%%%%%%%%%%%%%%%%%%%% Here come the atomic numbers of the atoms involved% atomTypeSc H% EndAtomType%%%%%%%%%%%%%%%%%%%%% valences【是赝势的价电子数目吗？No,指汉典元素周期表中对应的氧化态。如何改变氧化态？同时具有+2,+3价的元素如何处理？】3 1% endValences******************************************* & & & & & & & POPULATION & & & & & & & *******************************************30 & &: populationSize (how many individuals per generation)100 & : initialPopSize 30 & &: numGenerations (how many generations shall be calculated)25 & &: stopCrit ******************************************% & & & FIRST VAR. COMP. GENERATION & & &*******************************************20 & &: firstGeneMax (how many different compositions for first generation)8 & & : minAt (minimum amount of atoms/cell for first generation) 16 & &: maxAt (maximum amount of atoms/cell for first generation) &【可能需根据实际情况指定？】【USPEX中如何实现变胞？8，16表达了什么含义？】******************************************* &SURVIVAL OF THE FITTEST AND SELECTION *******************************************0 & & : reoptOld 0.6 & : bestFrac ************************************************************************************* & & & & &VARIATION OPERATORS & & & & & *************************************************************************************0.50 &: fracGene (fraction of generation produced by heredity)0.20 &: fracRand (fraction of generation produced randomly from space groups)0.20 &: fracAtomsMut (fraction of the generation produced by softmutation)0.10 &: fracTrans (fraction of the generation produced by transmutations)***************************************** & & & & & & CONSTRAINTS & & & & & & &*****************************************1.5 & : minVectorLength ( minimal length of any lattice vector)%%%%%%%%%%%%%%%%% IonDistances1.44 &088 0.0 0.32% EndDistances% &汉典元素周期表中的共价键长：或参考&&%%%%%%%%%%%%%%%%****************************************** & & & & & & & & CELL & & & & & & & & &******************************************% The following is what you know about the lattice. If you know the lattice% vectors, type them in as 3x3 matrix. If not, type the estimated volume.% For variable composition - type the estimated atomic volume for each element.% Latticevalues (this word MUST stay here, type values below)177% Endvalues (this word MUST stay here)%日本NIMS数据库：找到对应物质的模型结构，下载cif 文件，通过VESTA看体积数据 ****************************************** & DETAILS OF AB INITIO CALCULATIONS & * *****************************************% supported: &1-vasp, 2-siesta, 3-gulp, 4-LAMMPS, 5-NeuralNetworks% 6-dmacrys, 7-cp2k, 8-QuantumEspresso, 9-ASE, 10-ATK, 11-CASTEPabinitioCode (which code from CommandExecutable shall be used for calculation? )1 1 1 1 1ENDabinit%Resolution for KPOINTS - one number per step or just one number in total)% KresolStart0.16 0.12 0.10 0.08 0.06% &Kresolend% commandExecutablevasp% mpiexec -n 8 -machinefile .nodelists vasp & out.vaspmpiexec &-np 8 vasp &log% EndExecutable5 & & : numParallelCalcs (how many parallel calculations shall be performed)1 & & : whichCluster (0: no-job-script, 1: local submission, 2: remote) & & 【matlab语法，‘：’的作用】submission)0.010 : toleranceFing (tolerance for identical structures)****************************************** & & & & & & & RESTART & & & & & & & & ******************************************0 & &: pickUpYN (if pickUpYN~=0 , then a previous calculation will be continued )0 & &: pickUpGen (at which generation shall the previous calculation be picked up? If = 0 , then a new calculation is started)0 & &: pickUpFolder (number of the results folder to be used. If = 0 , then the highest existing number is taken)手册摘录解读：Specify the following varcomp-only options: variable &firstGeneMax
【变量 &第一代产生的different compositions数量】Meaning: How many different compositions 【怎样确保产生自己想要的组成？！】are sampled in the first generation. If 0, then the number is equal to initialPopSize/4. For binaries, we recommend firstGeneMax=11, for ternaries a higher value is needed, e.g. 30. Default: 11Format: 10 : firstGeneMaxvariable &minAtMeaning: Minimum number of atoms (for calculationType=301/201/300) or molecules (for calculationType=311) in the unit cell for the first generation. Default: No defaultFormat: 10 : minAtvariable
&maxAtMeaning: Maximum number of atoms (for calculationType=301/201/300 or in META calculations) or molecules (for calculationType=311) in the unit cell for the first generation. Default: No default & 【没有默认值，需自己指定】Format: 20 : maxAt根据自己服务器提交VASP任务脚本修改的submitJob_local.m文件function jobNumber = submitJob_local()%-------------------------------------------------------------%This routine is to check if the submitted job is complete or not%One needs to do a little edit based on your own situation.%1 & : whichCluster (default 0, 1: local submission, 2: remote submission)%-------------------------------------------------------------%Step 1: to prepare the job script that is required by your supercomputerfp = fopen('myrun', 'w'); & &fprintf(fp, '#!/bin/sh\n');fprintf(fp, '#PBS -l nodes=1:ppn=8,walltime=1:30:00 -q cfn_short\n');fprintf(fp, '#PBS -N USPEX\n');fprintf(fp, '#PBS -j oe\n');fprintf(fp, '#PBS -V \n');fprintf(fp, '#PBS -q dell \n');fprintf(fp,'#PBS -S /bin/bash \n');fprintf(fp, 'cd ${PBS_O_WORKDIR}\n');fprintf(fp, 'mpiexec -np 8 vasp & vasp.out\n');fclose(fp);%Step 2: to submit the job with a command like qsub, bsub, llsubmit, etc.[a,b]=unix(['qsub myrun'])%Step 3: to get the jobID from the screen message%It will output some message on the screen like '2350873.nano.cfn.bnl.local'end_marker = findstr(b,'.');jobNumber = b(1:end_marker(1)-1); 为保证程序周期性执行，修改并执行下述脚本，nohup ./run-uspex.sh && &：cat run-uspex.sh #!/bin/shwhile truedo & date && log
& /opt/matlab2013/bin/matlab && USPEX.m &&log
& sleep 300doneUSPEX问答： &最近在使用USPEX遇到以下两个问题，期盼您的解答： & &1) 怎样限制USPEX提交的任务数量，即始终保持只有五个任务在队列中排队或运算，而不是像下述情形一样，有上百个任务在队列中： & & &50375.mu01 &yexq dell & & vasp & &12 & &-- &7200: R 47:2550443.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50444.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50445.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50446.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50447.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50448.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50449.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50450.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50451.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50452.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50453.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- ......&&2) &IonDistances离子之间距离，感觉应该是共价半径的加和，不知对否？Answer &from &Lirong Han(1)这个我还真不知到在哪里设置，我用的都是已经写好的脚本，您可以查一下手册，上面应该有写。(2) 一般设置为离子半径的平均值，实际只要在差不多的范围内就没有关系From &Xing Wang#!/bin/sh#PBS -l nodes=1:ppn=12#PBS -N UZr2_phonon#PBS -j oeexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/software/compiler/mkl/lib/em64tcd $PBS_O_WORKDIRNPROCS=`wc -l & $PBS_NODEFILE`echo This job has allocated $NPROCS nodesecho The root node isuname -nmaster=`hostname | cut -f 1 -d '.'`node_list=`cat $PBS_NODEFILE`##cat $PBS_NODEFILE | awk '{ print $1&-clust& }' & ./hostfilecat $PBS_NODEFILE | awk '{ print $1& slots=12& }' & ./hostfile/home/software/mpi/openmpi1.4.3-intel/bin/mpirun &-np $NPROCS -hostfile ./hostfile /home/software/vasp/vasp.5.2.2/vasp &&vasp.logrm hostfile vasp.log &EIGENVAL DOSCAR &IBZKPT WAVECAR CHG CHGCAR XDATCAR PCDAT Thanks to QiangZhu and XInyue CHen & &1) 怎样限制USPEX提交的任务数量，即始终保持只有五个任务在队列中排队或运算，而不是像下述情形一样，有上百个任务在队列中： 具体设置请见： 关键就是你要修改 checkStatus_local.m%Step1: the command to check job by ID. & & [a,b] = unix(['qstat ' jobID ''])如果你用qstat查命令就不用修改%Step2: to find the keywords from the screen message to determine if the job is complete%Below is just a sample:%-------------------------------------------------------------------------------%Job id & & & & & & & & & &Name & & & & & & User & & & & & &Time Use S Queue%------------------------- ---------------- --------------- -------- - ---------%2455453.nano & & & & & & &USPEX & & & & & &qzhu & & & & & &02:28:42 R cfn_gen04%------------------------------------------------------------------------------- & &if isempty(findstr(b,'R cfn_')) & isempty(findstr(b,'Q cfn_')) & 这里我找的是如果改作业状态不是在（Run）后者（Queue），就认为作业结束， 你需要对关键词修改即可50375.mu01 &yexq dell & & vasp & &12 & &-- &7200: R 47:2550443.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50444.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50445.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50446.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50447.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50448.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50449.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50450.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50451.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50452.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- 50453.mu01 &yexq dell & & USPEX & &8 & &-- &01:30 Q & -- ......（程xy博士：这个好像要修改提交的脚本，具体哪个跟每个超级机有关...你需要修改uspex根目录下的submission里面的相关文件这个比较复杂，最好问问ZhuQ博士）2) &IonDistances离子之间距离，感觉应该是共价半径的加和，不知对否？（程xy博士：是共价半径的0.8倍，估计值） &0.6-0.8倍的区间都可以USPEX目录下的文件及文件夹： lsAntiSeeds & & & &Current_POP.mat &getStuff & &multiple_runs &results1 & & &Submission & & & & USPEX.mclean & & & & & &ev_alg.m & & & & INPUT.txt & nohup.out & & &run-uspex.sh &submitJob_local.m &uspex_MoSi2clean_tough & & &FunctionFolder & log & & & & out.uspex & & &Seeds & & & & submit.shCurrent_ORG.mat &getFromTo & & & &metasoft.m &out.uspex2 & & Specific & & &test运行后产生Cal*等文件夹。变胞方法： 参考uspex手册 & &
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Copyright &USPEX算例简介
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关注：1) USPEX、CALYPSO等的最新发表文章2) USPEX、CALYPSO等的经典算例分析附-各算例简介：&*****************************************************Here we give examples of calculations using USPEX.*****************************************************We recommend that before doing production calculations, you try to run these tests to make sure that everything works. If any problems, contact us. We also recommend that when you do production calculations, you start with one of these &test& folders and edit input files - instead of creating them from scratch.Before testing, put executables of VASP, SIESTA, GULP,... (whichever codes you are using) in folders Specific as ./Specific/vasp, ./Specific/siesta, ./Specific/gulp. 【将可执行文件拷入Specific目录，不是必须的？】To run USPEX, simply type:nohup matlab & USPEX.m & log &(or analogous command line with Octave). Well, this is described in the Manual - and before doing anything, you should read the Manual!When analyzing your tests - you can compare your results with the &standard& testing results that can be found in folders &reference&.Folders AuxiliaryFiles and generationNN are removed from reference in all tests (except test #4) to decrease the size of the test folders.Most tests are tailored to be fast, rather than accurate or physically meaningful. They test the basic machinery - the variation operators and different functionalities of the code. Keep this in mind! Most tests here are done with GULP, whose speed is ideal for testing purposes. But beware - most of the standard interatomic potentials result in wrong ground states! For MgAl2O4 the Buckingham potential we used in these tests gives reasonable structures at high pressures, but fails at low pressure!!! &If you want good results, you should have &more expensive& calculations and should use ab initio calculations.【如何在保持结果准确性的前提下，提高计算效率，节省时间】Also, in real calculations you should not stop the code after 5-10 generations (as is done in some of the examples). Please giveUSPEX some time to explore the energy landscape and find with confidence the globally optimum solution.+++++++++++++++++LIST OF TESTS:+++++++++++++++++(**)T0_Physics_VASP: Silicon (8 atoms/cell) at zero pressure.
Variable-cell DFT calculation using VASP, PBE96 functional. Many thanks to G.Kresse for permission to include his PAW files (POTCAR) in our distribution. &Test created by ARO, updated by AOL and ARO.(**)T1_Physics_GULP: MgAl2O4 (28 atoms/cell) at 100 GPa pressure. Variable-cell calculation using Buckingham potentials, GULP code. This test has direct bearing on the physics of the Earth's interior! Test created by ARO, updated by AOL and ARO. &(**)T2_conv_GULP: this example shows how to do structure prediction when you know cell parameters. MgSiO3 (20 atoms/cell) with Buckingham potentials, GULP code. Cell parameters correspond to post-perovskite. Test created by ARO, updated by AOL and ARO.(**)T3_antiseeds_GULP: Calculations for Lennard_Jones nanoparticle with 38 atoms are done with different antiseeds (ageing) settings. 【什么是antiseeds ？！】(**)T4_restart_GULP: this example shows how to restart from a previous calculation. The previous results are in folder results1, and when you run folder results2 appears. MgAl2O4 (14 atoms/cell) at 100 GPa pressure. Variable-cell calculation using Buckingham potentials, GULP code. Test created by ARO, updated by AOL.!!! IMPORTANT !!! You can not restart matlab calculation using octave and octave calculation using matlab, since the formats of .mat files aredifferent. Therefore please use the appropriate results1 folder (rename results1_octave into results1 default results1 isthe matlab calculation).【不明白】(**)T5_seeds_GULP: this example shows how to use seed structures (i.e. starting not from fully random structures, but to include some structures that you think might be reasonable). Seed structures are given in the file Seeds/POSCARS. MgAl2O4 (14 atoms/cell) at 100 GPa pressure. Variable-cell calculation using Buckingham potentials, GULP code. Test created by ARO, updated by AOL. &【Seed structures 不是必须的？】(**)T6_hardness_GULP: this test shows the optimisation of hardness (search for hardest structure in a given chemical system). MgO (8 atoms/cell). Variable-cell calculation using Buckingham potentials, GULP code. Test created by ARO, updated by AOL and ARO.Based on GULP and hardness formula of Li (2009) embedded in valence-topological approach of Lyakhov and Oganov ().&(**)T7_varcomp_GULP: Lennard-Jones binary system, GULP, and variable-composition method of Wang, Lyakhov and Oganov (, 2012). Test created by ARO, updated by AOL. (**)T8_clusters_GULP: cluster (nanoparticle) structure optimisation. Lennard-Jones cluster with 13 atoms. GULP code. Test created by AOL.(**)T9_GULP_VASP: Calculations in which optimisation starts with GULP and the last step is done with VASP for better accuracy. Test created by ARO, updated by AOL and ARO. This test is very short - only 5 generations, just to test the gulp-vasp functionality.(**)T10_Performance_GULP: SrTiO3 (50 atoms/cell) at zero pressure. Variable-cell calculation using Buckingham potentials, GULP code. Running this test you can see that even for such a relatively large system USPEX code scores a &90% success rate and remarkable efficiency. This contrasts with a 7-12% success rate reported for the same system and using the same potential by Zurek & Lonie. Clearly, USPEX outperforms the poor reimplementation of our method by Zurek and Lonnie. We have witnessed excellent performance of our code also for much larger systems. Test created by ARO, updated by AOL. (**)T11_molecule_DMACRYS: Methane molecular crystal with 8 molecules in the variable unit cell. Molecule is described in the file MOL_1. DMACRYS code is used for optimization. Please put executables dmacrys, neighcrys-pp, neighcrys-vv in the folder Specific. Test created by Q. Zhu.(**)T12_molecule_VASP: Methane molecular crystal with 4 molecules in the variable unit cell. The input is similar to that in T11, except VASP code is used for optimization. Test created by Q. Zhu.(**)T13_Castep: Carbon (8 atoms/cell) at zero pressure. Variable-cell DFT calculation using CASTEP. Test created by Z. Raza and X. Dong.(**)T14_Physics_PSO_GULP: MgAl2O4 (28 atoms/cell) at 100 GPa pressure. Variable-cell calculation using Buckingham potentials, GULP code. Optimization is done using the Particle Swarm Optimization (PSO) algorithm of Lyakhov and Oganov (2012), which introduces important corrections toearlier PSO algorithm of Boldyrev (and a very similar to it algorithm of Wang-Lv-Zhu-Ma). To activate it, file PSO_input has to be present in the main folder. Test created by AOL.(**)T15_random_sampling_GULP: Test of random sampling approach (one large generation) with symmetric initialization (Zhu et al(2012), Lyakhov et al (2012)).Shortened form of the input file is used (most parameters are default ones in this case).MgAl2O4 (14 atoms/cell) at 100 GPa pressure. Variable-cell calculation using Buckingham potentials, GULP code. Test created by AOL. (**)T16_metadynamics_GULP: Evolutionary metadynamics (Zhu, Oganov, Lyakhov (2012)) illustrated for MgSiO3 (20 atoms/cell) using the GULP code. The initial structure should be provided in the vasp 5.2 format (i.e. with added line containing element names) in the file POSCAR_1. Test created by Zhu. (**)T17_order_optimization_GULP: Optimization of the structural order (Oganov and Valle (2009); Lyakhov Oganov Valle (2010)) for MgAl2O4 (14 atoms/cell) at 100 GPa pressure. Variable-cell calculation using Buckingham potentials, GULP code. Note that the most ordered structure is not the ground state for this system! Test created by AOL.(**)T18_order_without_relaxation: Optimization of the structural order (Oganov and Valle (2009); Lyakhov Oganov Valle (2010)) without relaxation (abinitioCode = 0). Seed structure (supercell of Ti-Cu-O-structure) is permutated in a search of the permutant with the minimum/maximum order. Minimizing order in this situation, one gets a generalized version of the &special quasirandom structure&. Test created by AOL and ARO.(**)T19_QuantumEspresso: Carbon (8 atoms/cell) at zero pressure. Variable-cell DFT calculation using Quantum Espresso. Test created by AOL.(**)T20_ATK: Carbon (8 atoms/cell) at zero pressure. Variable-cell DFT calculation using ATK. Test created by X Dong.(**)T21_Lammps: Carbon (16 atoms/cell) at zero pressure. Variable-cell. Test created by X Dong.(**)T22_VCNEB: Test of AlN B3-&B1 phase transition at 14GPa. &Test created by Qian.**********************************************NOTE: USPEX works with a variety of other codes (CP2K, MD++). We will include test cases for at least some of these codes gradually.
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