# Open SourceMolecular Dynamics

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exercises:2018_ethz_mmm:re_2018

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 — exercises:2018_ethz_mmm:re_2018 [2018/05/18 03:08] (current)dpasserone created 2018/05/18 03:08 dpasserone created 2018/05/18 03:08 dpasserone created Line 1: Line 1: + ====== Replica exchange of the disordering of a cluster ====== + + + For this job we will use the cluster **HYPATIA** available at Empa. There we have access to parallel facilities with reserved nodes for the lecture. + How to connect to **HYPATIA**:​ + + Dear Student, ​ + + In order to be able to run simulations at high priority, today we will work on the Empa Cluster. ​ + We have created a personal account for you. Since the cluster is behind a firewall, we must connect to a gate machine (jumphost) to be allowed to access to the cluster. ​ + + Here the instructions to connect. ​ + + 1) Decide a username for hypatia (it will be one between mmmstud01 and mmmstud25 ) + 2) connect to the jumphost with the username (same for all) **mmmstud** + + ssh -X mmmstud@jump1.empa.ch ​ + Password: will be communicated in the class + + + + + 3) Connect to hypatia: + ssh -X mmmstud02@hypatia (replace "​02"​ by your number) + password: same as username + + 4) you are in! + + ​ + ============================================ + + + + [you@hypatia ~]$mmm-init + [you@hypatia ~]$ cd /​mnt/​scratch/​YOURUSER/​ + [you@hypatia ~]$cp -r /​mnt/​scratch/​psd/​exercise_11.1 . + [you@hypatia ~]$ cd exercise_11.1 + ​ + + + The commands that you need to do to perform the exercise are, in this order: + + + [you@hypatia ~]$qsub 00_run + [you@hypatia ~]$ ./​01_adapt_files + [you@hypatia ~]$./​02_reorder + [you@hypatia ~]$ ./​03_extract_allaverages + ​ + + ===== Running the job ===== + + The script contains the directives for the queuing system, including 16 cores on one nodes reserved for the job. + + + #=== job name: + #PBS -N parallel ​ + #=== wall time limit (h:m:s) + #PBS -l walltime=1:​00:​00 + #choice of the number of nodes and proc. per node + #PBS -l nodes=1:​ppn=16 ​ + #PBS -q short + #which queue + #=== memory usage + ##PBS -l mem=1024mb + #=== join stdout and stderr + #PBS -j oe + #​====================================== + + # + # set environment variables + # + + module unload mvapich2 + module load openmpi + module load lammps/​17Nov16/​openmpi/​2.0.1/​gcc/​4.9.4 + cd $PBS_O_WORKDIR ​ ​ + + rm parallel.o* log.* screen* + + mpiexec -np 16 lmp_mpi -partition 16x1 -in input + ​ + + The last line is the command to run a parallel lammps job with the input file ''​input''​ + + ===== The input file for lammps ===== + + + The file input contains information for the program **lammps**. Details on the documentation can be found [[http://​lammps.sandia.gov/​doc/​Manual.html|here]] + + There is an initialization section, showing the kind of units (see [[http://​lammps.sandia.gov/​doc/​units.html|this page]]), the dimensionality,​ the boundary conditions. ​ + + <​code>​ + # Initialization + units metal + dimension ​ 3 + boundary ​ p p p + atom_style ​ ​atomic + ​ + + In the second part of the input file a spherical region is defined (to confine the cluster). Then the atoms are read from ''​input.dat''​. We also assign a mass to the kind number **1** (there is just one atomic type for Argon). ​ + + + <​code>​ + region rs sphere 0 0 0 12.66 + read_data ​ input.dat + mass 1 39.948 + ​ + + Then, we define the parameters for the Lennard-Jones potential. The units are **eV** for epsilon, and angstrom for **sigma**. ​ + The last number is the cutoff, in Angstrom. ​ + + <​code>​ + pair_style lj/cut 8.5 + pair_coeff 1 1 0.01042 3.405 8.5 + ​ + + Then, we initialize the ''​fix''​ and the velocity as well as the temperature of each replica, which have been previously generated using the program **t.x** present in the same directory. We distribute the temperature exponentially between 2 K and 40 K. In LAMMPS, a ''​fix''​ is any operation that is applied to the system during timestepping or minimization. Here we have a ''​fix''​ for controlling temperature with NVT (a different temperature for each temperature),​ and a ''​fix''​ for applying a harmonic restraint to the spherical region confining the cluster. In this way, the atoms going beyond this region will be elastically pushed back into the sphere. ​ + + <​code>​ + variable i equal part + variable t world 2.00 2.44 2.98 3.64 4.45 5.43 6.63 8.09 9.88 ​12.07 ​ ​14.74 ​ ​17.99 ​ ​21.97 ​ ​26.83 ​ ​32.76 ​ 40.00 + velocity ​ all create ​$t        293288 + velocity all zero linear + velocity all zero angular + fix        1        all        nvt        temp        $t$t        0.1 + fix  2 all wall/region rs harmonic 2.0 0.0 0.4 + ​ + + The next section is about writing out each 1000 steps the relevant information about temperature and energy. We also dump a restart file at the end, and every 10000 steps a structure in xyz format. ​ + + <​code>​ + thermo ​        1000 + thermo_style ​       custom ​       step  temp     pe ke etotal + thermo_modify ​      ​line ​       one + restart 5000000 restart.* + dump         2 all xyz 10000 structure_$i.xyz + dump_modify ​ 2 element "​Ar"​ sort id + ​ + + Finally, this is the command to run the tempering, with an exchange move attempted every 1000 step of molecular dynamics and an initial temperature$t that is different from replica to replica. The last numbers are random seeds that are used for choosing which replica to exchange and for the Metropolis criterion. + + <​code>​ + temper 5000000 1000 $t 1 3678 3490 + ​ + + ===== Adapting the output files ===== + + We must now make some postprocessing on the output files. The goal is to performs averages at different temperatures. These averages are enhanced by the exchanges that were performed between different molecular dynamics replica. Note that temperature is set by a thermostat. ​ + + + **Example**. Processor 0 starts with temperature T0=2 K, processor 1 with temperature T1=2.44 K. + After 1000 steps, an exchange step is attempted and accepted with some probability (see theory slides, and also the paper + [[doi>​10.1063/​1.481671]]. After the exchange move, the temperature of processor 0 is 2.44 and the one of processor 1 is 2 K. + But you can see it also as the **configurations** of T0=2 K and the one of T1=2.44 K are changing, thus improving the sampling at both temperature. + ​ + + The script ''​01_adapt_files''​ performs the following operations: + + + - prunes the ''​log.lammps''​ file which contains a log of all exchanges between the replicas. Take only the steps for which we also have a dump of the atomic coordinates. + - For all the ''​log.lammps.*''​ files from each replica take only the lines for which we also have a dump of the atomic coordinates. These lines are put in a file *.nxyz, one for each replica. Each line contains temperatures,​ potential energies, etc. + - Compute the **q4** order parameter for all structure files and create ''​*.q4''​ files, one for each replica. + - now paste the ''​*.nxyz''​ and the ''​*.q4''​ files into a file ''​t_q4_epot_etot.*.out''​ containing the dump of temperature,​ energy, q4 every 10000 steps. + ​ + + + ===== Reordering the replica: one temperature,​ one file ===== + + At this point, we have a set of ''​t_q4_epot_etot.*.out'',​ one for each replica (processor). But along each of these files, the temperatures change a lot due to the exchanges. So, we use the file ''​exchanges_nxyz.log''​ that keeps track of the exchanges, and tells us at a given timestep which replica has which temperature:​ we scramble the ''​t_q4_epot_etot.*.out''​ files, and at the end we will have one file for each temperature. This is accomplished by the script ''​02_reorder''​. ​ + + + * Consider each file t_q4_epot_etot.*.out (processor by processor). Say you consider the number 5 (6th replica): ''​t_epot_q4_etot.5.out''​. + * At the step 50000, the file shows the following line: + ''​50000 6.7133746 -1.7636174 0.189 -1.7315099''​ + + indicating a temperature of 6.7133746. ​ + * The file ''​exchanges_nxyz.log'',​ at the step 50000, gives us the following line: + ''​50000 7 0 3 2 1 6 10 5 12 8 11 4 9 13 15 14''​ + + indicating that at the 6th replica (column **7**), we have the temperature **6**, which is (see input file) T=6.63 K. Meaning that at step 50000, the thermostat is keeping replica 5 around the temperature T=6.63 K. + * This means that this line has to be stored in the temperature file number **6**. ​ + ​ + + At the end of the above procedure performed by the small script section: + + NP=16 + NP1=$[NP-1] + rm torder* + for repl in seq 0 $NP1 + do + echo$repl + awk -v rep=$repl '​{r2=rep+2;​print$r2}' ​ < exchanges_nxyz.log ​ > rep_$repl + i=0 + for a in cat rep_$repl + do + i=$[i+1] + head -$i t_q4_epot_etot.$repl.out | tail -1 >> torder.$a + done + done + ​ + + we will have a set of files, one for each temperature. The file **torder.6** (showing the temperature log around **T=6.63 K** shows something like that: + <​code>​ + 110000 6.0832407 0.188 -1.7669426 -1.7378488 + 300000 5.3292135 0.189 -1.7741021 -1.7486144 + 460000 7.270977 0.188 -1.7594967 -1.7247223 + 850000 5.547995 0.189 -1.7583209 -1.7317869 + 900000 6.0463203 0.190 -1.7563726 -1.7274553 + 1100000 7.4527984 0.189 -1.7608437 -1.7251998 + 1160000 7.660013 0.189 -1.7653205 -1.7286855 + 1290000 7.634912 0.188 -1.7551173 -1.7186023 + 1520000 6.7791476 0.190 -1.7719473 -1.7395252 + 1530000 5.562028 0.189 -1.7551797 -1.7285786 + 1540000 5.9499865 0.189 -1.7682706 -1.739814 + 1560000 8.0181451 0.186 -1.7549744 -1.7166267 + 1670000 6.4413007 0.189 -1.7601051 -1.7292988 + 1740000 5.5362416 0.188 -1.7592589 -1.7327812 + 1750000 6.8539271 0.189 -1.7645124 -1.7317327 + 2030000 7.8928443 0.188 -1.7657447 -1.7279962 + 2040000 5.3275227 0.189 -1.763795 -1.7383155 + 2100000 5.7265507 0.189 -1.7645332 -1.7371452 + 2550000 8.1985344 0.189 -1.7581595 -1.7189489 + 2580000 7.3481203 0.190 -1.7668799 -1.7317366 + 2780000 6.7587102 0.189 -1.7581622 -1.7258378 + 2800000 7.1581346 0.188 -1.7609368 -1.7267022 + ... + ​ + + As you see, the number of steps is not ordered. This is easily achieved by the last part of the script ''​02_reorder''​ + + + for repl in seq 0 $NP1 + do + sort -nk1 torder.$repl > temp + mv temp torder.$repl + done + ​ + + and now the same file **torder.6** shows the following lines: + <​code>​ + 0 6.5781351 0.191 -1.7950808 -1.7636201 + 10000 5.4632389 0.188 -1.7609687 -1.7348401 + 20000 5.498244 0.189 -1.7597787 -1.7334826 + 30000 5.5142334 0.190 -1.7559687 -1.7295962 + 40000 7.4876442 0.189 -1.7622814 -1.7264708 + 50000 6.7133746 0.189 -1.7636174 -1.7315099 + 60000 5.9256132 0.188 -1.7593177 -1.7309777 + 70000 5.8414791 0.182 -1.7619757 -1.7340381 + 80000 3.9373038 0.189 -1.7687489 -1.7499183 + 90000 9.949782 0.189 -1.7640962 -1.7165101 + 100000 7.5855163 0.189 -1.7616613 -1.7253826 + 110000 6.0832407 0.188 -1.7669426 -1.7378488 + 120000 7.047375 0.189 -1.7588753 -1.7251703 + 130000 6.3651424 0.188 -1.7596141 -1.729172 + 140000 8.268057 0.188 -1.7647263 -1.7251833 + 150000 5.9081219 0.189 -1.7641776 -1.7359213 + 160000 5.2026849 0.188 -1.7603192 -1.7354367 + 170000 7.1694387 0.190 -1.762217 -1.7279282 + 180000 5.3619579 0.188 -1.7596472 -1.7340029 + 190000 7.9061423 0.188 -1.7631399 -1.7253278 + 200000 8.0048742 0.188 -1.7612416 -1.7229573 + 210000 9.5218385 0.189 -1.758481 -1.7129416 + 220000 6.3793891 0.189 -1.7658995 -1.7353892 + 230000 7.5105967 0.189 -1.7545324 -1.7186121 + 240000 7.6066407 0.188 -1.7643938 -1.7280141 + 250000 5.969687 0.189 -1.7611185 -1.7325677 + 260000 6.6266784 0.189 -1.761914 -1.730221 + 270000 6.8500414 0.181 -1.7615648 -1.7288036 + 280000 4.0299504 0.187 -1.7663177 -1.747044 + ... + ​ + + ===== Extract averages ===== + Now we are ready to extract averages at each temperature. This is achieved by the m_* function **m_average** (hint: look for the code of this function in the file ''/​share/​apps/​m_functions.bash''​),​ which is used in the script ''​03_extract_allaverages''​. + + + . /​share/​apps/​m_functions.bash + rm averages_t_q4_epot_etot + for a in torder.? torder.?? + do + ​t=m_average$a 2 + ​q4=m_average $a 4 + ​epot=m_average$a 3 + ​etot=m_average $a 5 + echo$t $q4$epot \$etot  >> averages_t_q4_epot_etot + done + ​ + + At this point you have a file ''​averages_t_q4_epot_etot''​ with the corresponding averages for each temperature. ​ + + + + ===== ASSIGNMENTS ===== + + ​ + - Using ''​gnuplot'',​ plot the steps vs. q4 (columns 1 and 3) from the file ''​t_q4_epot_etot.0.out'',​ ''​t_q4_epot_etot.13.out'',​ ''​t_q4_epot_etot.15.out''​. Comment what you observe. + - Compare using gnuplot the plot of the nsteps vs. potential energy (columns 1 and 4) for ''​t_q4_epot_etot.13.out''​ and ''​torder.13''​. Comment the differences + - Plot the ''​q4''​ in ''​torder.0'',​ ''​torder.5'',​ ''​torder.10'',​ ''​torder.15''​. Comment the differences. + - Using the averages file, try to reproduce figure 2, top panel of the paper  [[doi>​10.1063/​1.481671]]. + - ** ADVANCED **. Describe what you would need to reproduce Fig. 1 of the same paper. What does this figure show? Find the reference to this figure in the text of the paper. ​ + - ** ADVANCED **. Using the ''​torder.*''​ files, and using eq. (14), obtain Fig. 1 of the paper. ​ +
exercises/2018_ethz_mmm/re_2018.txt · Last modified: 2018/05/18 03:08 by dpasserone