├── LICENSE ├── README.md └── harmonic ├── compute_transmission.py ├── lammps_input_files ├── in.data ├── in.forces ├── in.relax └── in.vels ├── si.lammps └── subroutines.py /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. By contrast, 15 | the GNU General Public License is intended to guarantee your freedom to 16 | share and change all versions of a program--to make sure it remains free 17 | software for all its users. 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Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # phonon-transmission 2 | Harmonic phonon transmission calculations from molecular dynamics trajectories 3 | 4 | # harmonic 5 | Within harmonic are the codes 'compute_transmission.py' and 'subroutines.py'. 'subroutines.py' is a module that 'compute_transmission.py' calls. The module does most of the work, the compute code is where you provide simulations parameters that the code needs. The it mainly reads data in and plots it. The subdirectory scripts contains another directory, 'matlab', that has a matlab version of the code and some other functions that are useful. ORIGINAL_CODES contains the original code that my codes are based off. Also, compactify.cpp shoulde by compiled and used (USAGE: a.x vels.dat vels.dat.compact) to 'compactify' the velocity data into a more easy to read (for the code!) version. The subdirectory 'lammps_input_files' has lammps input scripts that produce the data for the transmission calculation. 6 | 7 | -------------------------------------------------------------------------------- /harmonic/compute_transmission.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | # -*- coding: utf-8 -*- 3 | """ 4 | Created on Mon Mar 11 10:36:56 2019 5 | 6 | @author: Ty Sterling 7 | ty.sterling@colorado.edu 8 | 9 | Another go at harmonic tr, bump hasn't gone away 10 | 11 | This is the main function calling from the module 12 | """ 13 | 14 | import numpy as np 15 | import sys 16 | import subroutines as fx 17 | import matplotlib.pyplot as plt 18 | fx.tic() 19 | 20 | ##### SIMULATION PARAMETERS ##### 21 | dT = 60 #NEMD bath temperature difference 22 | 23 | dtMD = 0.5e-15 #MD timestep 24 | dn = 2**5 #frequency velocities are printed 25 | dt = dtMD*dn #effective timestep for velocity data 26 | steps = 2**25 #number of simulation steps 27 | 28 | split = 20 #number of chunks to split data into for averaging 29 | tn = int(steps/dn/split) #number of steps per block of data 30 | 31 | win = 0.05 #gaussian smoothing width = THz 32 | kb = 1.38063e-23 #Boltzmann's constant, J/K 33 | 34 | forcefile = 'Fij.dat' 35 | velsfile = 'vels.compact.dat' 36 | outfile = 'si.1nm.prist.dat' 37 | 38 | conv = 1.602e-19/1e-24 #convert: v*dF/du*v = [A/ps]*[eV/A]/[A]*[A/ps] 39 | # eV/ps^2; 1 eV = 1.602e-19 J, 1 ps = 1e-12 s 40 | 41 | ##################################################################### 42 | #-------------------------------------------------------------------- 43 | ##################################################################### 44 | ## Print parameters to screen 45 | fx.printParams(dtMD,dt,dT,steps,split,tn) 46 | ## Generate time and freq. arrays 47 | om, thz, dom = fx.makeTime(dt,tn) 48 | ## Get force constants from file 49 | print(('\tNow reading force constants from '+str(forcefile)+'')) 50 | kij, du, idsl, idsr, ids, nl, nr, n = fx.readFij(forcefile) 51 | fx.toc() 52 | 53 | ## Read velocites 54 | with open(velsfile,'r') as fid: 55 | if int(fid.readline().strip().split()[1]) != n: #error checking 56 | sys.exit('LAMMPS ERROR: Numer of atoms in vels run doesn\'t' 57 | 'match forces run') 58 | if int(fid.readline().strip().split()[1]) != dn: #error checking 59 | sys.exit('LAMMPS ERROR: Different stride given in ' 60 | +str(velsfile)) 61 | 62 | fid.readline() #skip comment 63 | for j in range(n): #read the ids for error checking 64 | if ids[j] != int(fid.readline().strip().split()[0]): 65 | sys.exit('LAMMPS ERROR: ids in '+str(velsfile)+' don\'t' 66 | ' match'+str(forcefile)) 67 | fid.readline() #skip comment 68 | 69 | ## Get velocities for each block 70 | qomRaw = np.zeros((tn,split)).astype(complex) 71 | for s in range(split): #loop over blocks for averaging 72 | vels = np.zeros((tn,n*3)) # [time,(1vx,1vy,1vz,2vx,2vy,...)] 73 | print(('\n\tNow reading velocities from block '+str(s+1)+'\n')) 74 | num = tn//10 75 | for j in range(tn): 76 | if j != 0 and j%(num) == 0: #print progress updates 77 | print(('\t\tNow '+str(10*np.round(j/num,decimals=1))+ 78 | '% done reading block '+str(s+1))) 79 | for k in range(n*3): 80 | vels[j,k] = float(fid.readline().strip().split()[0]) 81 | fx.toc() 82 | 83 | qomRaw[:,s] = fx.computeQ(kij,vels,om,idsl,idsr,nl,nr,tn,dt,s) 84 | fx.toc() 85 | #save each split into an array 86 | 87 | qomRaw = -2*conv*np.imag(qomRaw)/(tn*dt) 88 | qom = qomRaw.mean(axis=1) #avg across splits 89 | tr = qom/kb/dT #transmission 90 | 91 | ## Smoothen transmission 92 | tr = fx.gsmooth(tr,win,dom) #gaussian convolution 93 | ## Write to output file 94 | fx.writeTr(outfile,thz,tr,qom,dT,dtMD,tn,win) 95 | 96 | print('\n\tALL DONE!\n') 97 | fx.toc() 98 | 99 | ## Plot the results 100 | fig,ax = plt.subplots() 101 | ax.plot(thz,tr) 102 | plt.xlabel('THz') 103 | plt.ylabel('Transmission') 104 | plt.title('Interfacial Phonon Transmission') 105 | plt.show() 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | -------------------------------------------------------------------------------- /harmonic/lammps_input_files/in.data: -------------------------------------------------------------------------------- 1 | ########## required parameters ################## 2 | atom_style atomic 3 | units metal 4 | dimension 3 5 | boundary p p p 6 | processors * * * 7 | 8 | #-------- read restart file positions into memory 9 | shell rm data.restart 10 | 11 | read_restart restart 12 | pair_style tersoff 13 | pair_coeff * * SiCGe.tersoff Si(D) Ge 14 | 15 | #-------- write data file ------------------- 16 | write_data data.restart nocoeff 17 | 18 | -------------------------------------------------------------------------------- /harmonic/lammps_input_files/in.forces: -------------------------------------------------------------------------------- 1 | ######## simulation setup ################ 2 | variable T equal 300 3 | variable kB equal 8.6173324e-5 4 | variable A2m equal 1.0e-10 5 | variable ps2s equal 1.0e-12 6 | variable eV2J equal 1.60217646e-19 7 | variable convert equal ${eV2J}/${A2m}/${A2m}/${ps2s} 8 | 9 | # ----------- Basic setup ------------- 10 | atom_style atomic 11 | units metal 12 | dimension 3 13 | boundary p p p 14 | processors * 1 1 15 | atom_modify map hash 16 | read_data data.pos 17 | 18 | # ----------- Define potential and useful quantities ---- 19 | pair_style tersoff 20 | pair_coeff * * SiCGe.tersoff Si(D) Ge 21 | timestep 0.0005 22 | 23 | # ----------- Fix some atoms to avoid drift --------------- 24 | variable filetowrite string Fij.dat 25 | 26 | variable vac equal 20.0 27 | variable NX equal lx-${Vac} 28 | print ${NX} 29 | 30 | variable x_min equal (xlo+${vac}) 31 | variable x_max equal (xhi-${vac}) 32 | 33 | variable dmid equal 3 34 | variable xmid equal #NUM 35 | variable xmidL equal ${xinter}-0.05 36 | variable xmidR equal ${xinter}+0.05 37 | variable xmidlo equal ${xmid}-${dmid} 38 | variable xmidhi equal ${xmid}+${dmid} 39 | 40 | region left block ${xmidlo} ${xmidL} INF INF INF INF units box 41 | region right block ${xmidR} ${xmidhi} INF INF INF INF units box 42 | group interface_left region left 43 | group interface_right region right 44 | group interface union interface_left interface_right 45 | 46 | #------------------Compute Forces on atoms--------------- 47 | compute fxfyfz interface property/atom fx fy fz 48 | compute fxs interface property/atom fx 49 | compute fys interface property/atom fy 50 | compute fzs interface property/atom fz 51 | 52 | fix NVE all nve 53 | 54 | variable N equal "count(all)" 55 | variable NL equal "count(interface_left)" 56 | variable NR equal "count(interface_right)" 57 | 58 | #----------------------------Initialize groups-------------------------------------- 59 | 60 | group thisi id 1 61 | 62 | variable hstep equal 0.01 63 | variable hstepm2 equal -2*v_hstep 64 | 65 | shell rm ${filetowrite} 66 | 67 | dump helpdump interface custom 1 ${filetowrite} id c_fxs c_fys c_fzs 68 | dump_modify helpdump sort id 69 | dump_modify helpdump append yes 70 | 71 | #---------------- WRITE THE INTERFACE PARTICLES IDs and TYPEs TO ${filetowrite}--------- 72 | print "NL ${NL}" append ${filetowrite} 73 | print "NR ${NR}" append ${filetowrite} 74 | 75 | label loop1 76 | variable i1 loop $N 77 | variable xi equal x[${i1}] 78 | variable boolleft equal (${xi}<=${xmidL})&&(${xi}>=${xmidlo}) 79 | variable boolright equal (${xi}>=${xmidR})&&(${xi}<=${xmidhi}) 80 | if "${boolleft}" then & 81 | "print '${i1} 1' append ${filetowrite}" 82 | if "${boolright}" then & 83 | "print '${i1} 2' append ${filetowrite}" 84 | next i1 85 | 86 | jump SELF loop1 87 | 88 | #------------- Loop over atoms on one side, compute forces in all others ----------------- 89 | print "HSTEP ${hstep}" append ${filetowrite} 90 | thermo_modify flush yes 91 | 92 | variable counter equal 0 93 | 94 | label loop_i 95 | 96 | variable i loop $N 97 | variable xi equal x[${i}] 98 | variable boolleft equal (${xi}<=${xmidL})&&(${xi}>=${xmidlo}) 99 | variable boolright equal (${xi}>=${xmidR})&&(${xi}<=${xmidhi}) 100 | print '$i ${boolleft} ${boolright}' 101 | if "!${boolleft}" then & 102 | "next i" & 103 | "jump SELF loop_i" & 104 | "jump SELF final_break" 105 | 106 | group thisi delete 107 | group thisi id $i 108 | 109 | #---------------- X DIRECTION DISPLACEMENTS TO POSITIVE AND NEGATIVE DIRECTION------------------- 110 | 111 | displace_atoms thisi move ${hstep} 0 0 112 | variable counter equal ${counter}+1 113 | reset_timestep ${counter} 114 | print "counter=${counter}" 115 | run 0 # Update the forces in the compute 116 | 117 | displace_atoms thisi move ${hstepm2} 0 0 118 | variable counter equal ${counter}+1 119 | reset_timestep ${counter} 120 | print "counter=${counter}" 121 | run 0 # Update the forces in the compute 122 | 123 | displace_atoms thisi move ${hstep} 0 0 124 | 125 | #---------------- Y DIRECTION DISPLACEMENTS TO POSITIVE AND NEGATIVE DIRECTION--------------------- 126 | 127 | displace_atoms thisi move 0 ${hstep} 0 128 | variable counter equal ${counter}+1 129 | reset_timestep ${counter} 130 | print "counter=${counter}" 131 | run 0 # Update the forces in the compute 132 | 133 | displace_atoms thisi move 0 ${hstepm2} 0 134 | variable counter equal ${counter}+1 135 | reset_timestep ${counter} 136 | print "counter=${counter}" 137 | run 0 # Update the forces in the compute 138 | 139 | displace_atoms thisi move 0 ${hstep} 0 140 | 141 | #--------------- Z DIRECTION DISPLACEMENTS TO POSITIVE AND NEGATIVE DIRECTION---------------------- 142 | 143 | displace_atoms thisi move 0 0 ${hstep} 144 | variable counter equal ${counter}+1 145 | reset_timestep ${counter} 146 | print "counter=${counter}" 147 | run 0 # Update the forces in the compute 148 | 149 | displace_atoms thisi move 0 0 ${hstepm2} 150 | variable counter equal ${counter}+1 151 | reset_timestep ${counter} 152 | print "counter=${counter}" 153 | run 0 # Update the forces in the compute 154 | 155 | displace_atoms thisi move 0 0 ${hstep} 156 | 157 | next i 158 | jump SELF loop_i 159 | label final_break 160 | -------------------------------------------------------------------------------- /harmonic/lammps_input_files/in.relax: -------------------------------------------------------------------------------- 1 | ############ simulation setup ############# 2 | atom_style atomic 3 | units metal 4 | dimension 3 5 | boundary p p p 6 | processors * * * 7 | 8 | #---------- structure -------------------- 9 | read_data data.relax 10 | pair_style tersoff 11 | pair_coeff * * SiCGe.tersoff Si(D) Ge 12 | 13 | variable T equal 300 14 | timestep 0.0005 15 | 16 | ############# 0K relaxation ################# 17 | thermo_style custom step temp pe etotal press pxx pyy pzz lx ly lz fmax fnorm 18 | thermo 1000 19 | dump snap all custom 1000 snap.lammpstrj id type x y z 20 | 21 | #------- steepest descent ----------------- 22 | fix relax all box/relax x 0 y 0 z 0 couple none 23 | minimize 0.0 1.0e-9 100000 10000000 24 | min_style sd 25 | min_modify dmax 0.2 26 | 27 | ########### NPT relaxation ######################### 28 | fix NPT all npt temp $T $T $(dt*100) iso 0 0 $(dt*1000) 29 | run 2000000 30 | unfix NPT 31 | 32 | ########### NVE equilibration ###################### 33 | fix NVE all nve 34 | run 100000 35 | unfix NVE 36 | 37 | #-------------- write relaxed structure to data file ---------------- 38 | write_data data.pos nocoeff 39 | -------------------------------------------------------------------------------- /harmonic/lammps_input_files/in.vels: -------------------------------------------------------------------------------- 1 | ############## simulation setup ################### 2 | atom_style atomic 3 | units metal 4 | dimension 3 5 | boundary p p p 6 | processors * 1 1 7 | 8 | variable kB equal 8.6173324e-5 9 | variable a2m equal 1.0e-1 10 | variable ps2s equal 1.0e-12 11 | variable eV2J equal 1.60217646e-19 12 | variable convert equal ${eV2J}/${a2m}/${a2m}/${ps2s} 13 | 14 | #---------- system -------------------- 15 | read_data data.pos 16 | pair_style tersoff 17 | pair_coeff * * SiCGe.tersoff Si(D) 18 | 19 | #---------- temperature -------------------- 20 | timestep 0.0005 21 | variable T equal 300 22 | variable dT equal 30 23 | variable TR equal $T-${dT}/2 24 | variable TL equal $T+${dT}/2 25 | 26 | variable vac equal 20 27 | variable x_min equal xlo+${vac} 28 | variable x_max equal xhi-${vac} 29 | 30 | ########## Bath and fixed block definitions ################ 31 | variable aSi equal 5.431 32 | variable slab equal ${aSi} 33 | 34 | variable fixed equal ${aSi}*0.5 35 | variable baths equal ${aSi}*2 36 | 37 | variable x1 equal ${x_min}+${fixed} 38 | variable x2 equal ${x_max}-${fixed} 39 | variable x3 equal ${x1}+${baths} 40 | variable x4 equal ${x2}-${baths} 41 | region fix_L block INF ${x1} INF INF INF INF 42 | region fix_R block ${x2} INF INF INF INF INF 43 | region fix_both union 2 fix_L fix_R 44 | group fixed region fix_both 45 | group moves subtract all fixed 46 | 47 | ###### Velocity groups for transmission calculation ########### 48 | variable dmid equal 6 49 | variable xmid equal 26.47617 50 | variable xmidL equal ${xmid}-0.05 51 | variable xmidR equal ${xmid}+0.05 52 | variable xmidlo equal ${xmidL}-${dmid} 53 | variable xmidhi equal ${xmidR}+${dmid} 54 | 55 | region int_L block ${xmidlo} ${xmidL} INF INF INF INF units box 56 | region int_R block ${xmidR} ${xmidhi} INF INF INF INF units box 57 | group interface_L region int_L 58 | group interface_R region int_R 59 | group interface union interface_L interface_R 60 | 61 | ############################### NEMD calculation ####################################### 62 | 63 | #----------- heat reservoirs -------------------------------- 64 | region hotregion block ${x1} ${x3} INF INF INF INF 65 | group hot region hotregion 66 | region coldregion block ${x4} ${x2} INF INF INF INF 67 | group cold region coldregion 68 | 69 | ###### uncomment and use VMD to check that interface definitions are what you expect 70 | #group blocks union fixed hot cold interface 71 | #dump blocks blocks atom 10 blocks.lammpstrj 72 | ###### 73 | 74 | variable xlen equal ${x4}-${x3} 75 | variable cx equal ly*lz 76 | variable v equal xlen*cx 77 | 78 | # ----- write structure to file for VMD visualization ------ 79 | dump snap all atom 20000 snap.lammpstrj 80 | dump_modify snap append yes 81 | 82 | # ----------- Initialize velocities ---------------- 83 | velocity moves create ${T} ${SEED} mom yes rot yes dist gaussian 84 | velocity fixed set 0.0 0.0 0.0 units box 85 | 86 | # --------- thermalization ------------------------- 87 | variable Tis atom ${TL}-x/xhi*(${TL}-${TR}) 88 | fix NVE moves nve 89 | fix NVT moves langevin v_Tis 1.0 $(dt*100) ${SEED} 90 | fix freeze fixed setforce 0.0 0.0 0.0 91 | compute real_temp moves temp 92 | thermo_style custom step temp c_real_temp pe etotal press pxx pyy pzz 93 | thermo 10000 94 | thermo_modify flush yes 95 | 96 | run 250000 97 | unfix NVT 98 | 99 | #--------------- NEMD ------------------------- 100 | reset_timestep 1 101 | 102 | fix fcold cold langevin ${TR} ${TR} $(dt*100) ${langSEED} tally yes 103 | fix fhot hot langevin ${TL} ${TL} $(dt*100) ${langSEED} tally yes 104 | 105 | variable fluxout equal f_fcold/v_cx/step/dt*v_convert 106 | variable fluxin equal f_fhot/v_cx/step/dt*v_convert 107 | 108 | thermo_style custom step temp c_real_temp pe etotal press pxx pyy pzz f_fcold f_fhot v_fluxout v_fluxin 109 | thermo_modify flush yes 110 | 111 | compute ke moves ke/atom 112 | variable temp atom c_ke/1.5/v_kB 113 | compute cc1 moves chunk/atom bin/1d x lower ${slab} bound x ${x1} ${x2} units box 114 | fix cc1_T moves ave/chunk 1 200000 200000 cc1 v_temp file tmp.profile.0 115 | 116 | run 250000 117 | write_restart restart.stationary.* 118 | 119 | ########### Collect Velocities ############## 120 | variable dn equal 32 121 | dump vels interface custom ${dn} vels.dat id type vx vy vz 122 | dump_modify vels format line "%d %d %0.8g %0.8g %0.8g" 123 | dump_modify vels sort id 124 | 125 | run 524288 126 | write_restart restart.final.* 127 | -------------------------------------------------------------------------------- /harmonic/si.lammps: -------------------------------------------------------------------------------- 1 | 10x4x4 Silicon 2 | 3 | 1280 atoms 4 | 5 | 1 atom types 6 | 7 | 0.00000000 54.31000000 xlo xhi 8 | 0.00000000 21.72400000 ylo yhi 9 | 0.00000000 21.72400000 zlo zhi 10 | 11 | Masses 12 | 13 | 1 28.0855 14 | 15 | Atoms 16 | 17 | 1 1 0.00000000 0.00000000 0.00000000 18 | 2 1 0.00000000 2.71550000 2.71550000 19 | 3 1 2.71550000 0.00000000 2.71550000 20 | 4 1 2.71550000 2.71550000 0.00000000 21 | 5 1 1.35775000 1.35775000 1.35775000 22 | 6 1 4.07325000 4.07325000 1.35775000 23 | 7 1 1.35775000 4.07325000 4.07325000 24 | 8 1 4.07325000 1.35775000 4.07325000 25 | 9 1 0.00000000 0.00000000 5.43100000 26 | 10 1 0.00000000 2.71550000 8.14650000 27 | 11 1 2.71550000 0.00000000 8.14650000 28 | 12 1 2.71550000 2.71550000 5.43100000 29 | 13 1 1.35775000 1.35775000 6.78875000 30 | 14 1 4.07325000 4.07325000 6.78875000 31 | 15 1 1.35775000 4.07325000 9.50425000 32 | 16 1 4.07325000 1.35775000 9.50425000 33 | 17 1 0.00000000 0.00000000 10.86200000 34 | 18 1 0.00000000 2.71550000 13.57750000 35 | 19 1 2.71550000 0.00000000 13.57750000 36 | 20 1 2.71550000 2.71550000 10.86200000 37 | 21 1 1.35775000 1.35775000 12.21975000 38 | 22 1 4.07325000 4.07325000 12.21975000 39 | 23 1 1.35775000 4.07325000 14.93525000 40 | 24 1 4.07325000 1.35775000 14.93525000 41 | 25 1 0.00000000 0.00000000 16.29300000 42 | 26 1 0.00000000 2.71550000 19.00850000 43 | 27 1 2.71550000 0.00000000 19.00850000 44 | 28 1 2.71550000 2.71550000 16.29300000 45 | 29 1 1.35775000 1.35775000 17.65075000 46 | 30 1 4.07325000 4.07325000 17.65075000 47 | 31 1 1.35775000 4.07325000 20.36625000 48 | 32 1 4.07325000 1.35775000 20.36625000 49 | 33 1 0.00000000 5.43100000 0.00000000 50 | 34 1 0.00000000 8.14650000 2.71550000 51 | 35 1 2.71550000 5.43100000 2.71550000 52 | 36 1 2.71550000 8.14650000 0.00000000 53 | 37 1 1.35775000 6.78875000 1.35775000 54 | 38 1 4.07325000 9.50425000 1.35775000 55 | 39 1 1.35775000 9.50425000 4.07325000 56 | 40 1 4.07325000 6.78875000 4.07325000 57 | 41 1 0.00000000 5.43100000 5.43100000 58 | 42 1 0.00000000 8.14650000 8.14650000 59 | 43 1 2.71550000 5.43100000 8.14650000 60 | 44 1 2.71550000 8.14650000 5.43100000 61 | 45 1 1.35775000 6.78875000 6.78875000 62 | 46 1 4.07325000 9.50425000 6.78875000 63 | 47 1 1.35775000 9.50425000 9.50425000 64 | 48 1 4.07325000 6.78875000 9.50425000 65 | 49 1 0.00000000 5.43100000 10.86200000 66 | 50 1 0.00000000 8.14650000 13.57750000 67 | 51 1 2.71550000 5.43100000 13.57750000 68 | 52 1 2.71550000 8.14650000 10.86200000 69 | 53 1 1.35775000 6.78875000 12.21975000 70 | 54 1 4.07325000 9.50425000 12.21975000 71 | 55 1 1.35775000 9.50425000 14.93525000 72 | 56 1 4.07325000 6.78875000 14.93525000 73 | 57 1 0.00000000 5.43100000 16.29300000 74 | 58 1 0.00000000 8.14650000 19.00850000 75 | 59 1 2.71550000 5.43100000 19.00850000 76 | 60 1 2.71550000 8.14650000 16.29300000 77 | 61 1 1.35775000 6.78875000 17.65075000 78 | 62 1 4.07325000 9.50425000 17.65075000 79 | 63 1 1.35775000 9.50425000 20.36625000 80 | 64 1 4.07325000 6.78875000 20.36625000 81 | 65 1 0.00000000 10.86200000 0.00000000 82 | 66 1 0.00000000 13.57750000 2.71550000 83 | 67 1 2.71550000 10.86200000 2.71550000 84 | 68 1 2.71550000 13.57750000 0.00000000 85 | 69 1 1.35775000 12.21975000 1.35775000 86 | 70 1 4.07325000 14.93525000 1.35775000 87 | 71 1 1.35775000 14.93525000 4.07325000 88 | 72 1 4.07325000 12.21975000 4.07325000 89 | 73 1 0.00000000 10.86200000 5.43100000 90 | 74 1 0.00000000 13.57750000 8.14650000 91 | 75 1 2.71550000 10.86200000 8.14650000 92 | 76 1 2.71550000 13.57750000 5.43100000 93 | 77 1 1.35775000 12.21975000 6.78875000 94 | 78 1 4.07325000 14.93525000 6.78875000 95 | 79 1 1.35775000 14.93525000 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17.65075000 1.35775000 118 | 102 1 4.07325000 20.36625000 1.35775000 119 | 103 1 1.35775000 20.36625000 4.07325000 120 | 104 1 4.07325000 17.65075000 4.07325000 121 | 105 1 0.00000000 16.29300000 5.43100000 122 | 106 1 0.00000000 19.00850000 8.14650000 123 | 107 1 2.71550000 16.29300000 8.14650000 124 | 108 1 2.71550000 19.00850000 5.43100000 125 | 109 1 1.35775000 17.65075000 6.78875000 126 | 110 1 4.07325000 20.36625000 6.78875000 127 | 111 1 1.35775000 20.36625000 9.50425000 128 | 112 1 4.07325000 17.65075000 9.50425000 129 | 113 1 0.00000000 16.29300000 10.86200000 130 | 114 1 0.00000000 19.00850000 13.57750000 131 | 115 1 2.71550000 16.29300000 13.57750000 132 | 116 1 2.71550000 19.00850000 10.86200000 133 | 117 1 1.35775000 17.65075000 12.21975000 134 | 118 1 4.07325000 20.36625000 12.21975000 135 | 119 1 1.35775000 20.36625000 14.93525000 136 | 120 1 4.07325000 17.65075000 14.93525000 137 | 121 1 0.00000000 16.29300000 16.29300000 138 | 122 1 0.00000000 19.00850000 19.00850000 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47.52125000 1.35775000 20.36625000 1073 | 1057 1 43.44800000 5.43100000 0.00000000 1074 | 1058 1 43.44800000 8.14650000 2.71550000 1075 | 1059 1 46.16350000 5.43100000 2.71550000 1076 | 1060 1 46.16350000 8.14650000 0.00000000 1077 | 1061 1 44.80575000 6.78875000 1.35775000 1078 | 1062 1 47.52125000 9.50425000 1.35775000 1079 | 1063 1 44.80575000 9.50425000 4.07325000 1080 | 1064 1 47.52125000 6.78875000 4.07325000 1081 | 1065 1 43.44800000 5.43100000 5.43100000 1082 | 1066 1 43.44800000 8.14650000 8.14650000 1083 | 1067 1 46.16350000 5.43100000 8.14650000 1084 | 1068 1 46.16350000 8.14650000 5.43100000 1085 | 1069 1 44.80575000 6.78875000 6.78875000 1086 | 1070 1 47.52125000 9.50425000 6.78875000 1087 | 1071 1 44.80575000 9.50425000 9.50425000 1088 | 1072 1 47.52125000 6.78875000 9.50425000 1089 | 1073 1 43.44800000 5.43100000 10.86200000 1090 | 1074 1 43.44800000 8.14650000 13.57750000 1091 | 1075 1 46.16350000 5.43100000 13.57750000 1092 | 1076 1 46.16350000 8.14650000 10.86200000 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43.44800000 10.86200000 5.43100000 1114 | 1098 1 43.44800000 13.57750000 8.14650000 1115 | 1099 1 46.16350000 10.86200000 8.14650000 1116 | 1100 1 46.16350000 13.57750000 5.43100000 1117 | 1101 1 44.80575000 12.21975000 6.78875000 1118 | 1102 1 47.52125000 14.93525000 6.78875000 1119 | 1103 1 44.80575000 14.93525000 9.50425000 1120 | 1104 1 47.52125000 12.21975000 9.50425000 1121 | 1105 1 43.44800000 10.86200000 10.86200000 1122 | 1106 1 43.44800000 13.57750000 13.57750000 1123 | 1107 1 46.16350000 10.86200000 13.57750000 1124 | 1108 1 46.16350000 13.57750000 10.86200000 1125 | 1109 1 44.80575000 12.21975000 12.21975000 1126 | 1110 1 47.52125000 14.93525000 12.21975000 1127 | 1111 1 44.80575000 14.93525000 14.93525000 1128 | 1112 1 47.52125000 12.21975000 14.93525000 1129 | 1113 1 43.44800000 10.86200000 16.29300000 1130 | 1114 1 43.44800000 13.57750000 19.00850000 1131 | 1115 1 46.16350000 10.86200000 19.00850000 1132 | 1116 1 46.16350000 13.57750000 16.29300000 1133 | 1117 1 44.80575000 12.21975000 17.65075000 1134 | 1118 1 47.52125000 14.93525000 17.65075000 1135 | 1119 1 44.80575000 14.93525000 20.36625000 1136 | 1120 1 47.52125000 12.21975000 20.36625000 1137 | 1121 1 43.44800000 16.29300000 0.00000000 1138 | 1122 1 43.44800000 19.00850000 2.71550000 1139 | 1123 1 46.16350000 16.29300000 2.71550000 1140 | 1124 1 46.16350000 19.00850000 0.00000000 1141 | 1125 1 44.80575000 17.65075000 1.35775000 1142 | 1126 1 47.52125000 20.36625000 1.35775000 1143 | 1127 1 44.80575000 20.36625000 4.07325000 1144 | 1128 1 47.52125000 17.65075000 4.07325000 1145 | 1129 1 43.44800000 16.29300000 5.43100000 1146 | 1130 1 43.44800000 19.00850000 8.14650000 1147 | 1131 1 46.16350000 16.29300000 8.14650000 1148 | 1132 1 46.16350000 19.00850000 5.43100000 1149 | 1133 1 44.80575000 17.65075000 6.78875000 1150 | 1134 1 47.52125000 20.36625000 6.78875000 1151 | 1135 1 44.80575000 20.36625000 9.50425000 1152 | 1136 1 47.52125000 17.65075000 9.50425000 1153 | 1137 1 43.44800000 16.29300000 10.86200000 1154 | 1138 1 43.44800000 19.00850000 13.57750000 1155 | 1139 1 46.16350000 16.29300000 13.57750000 1156 | 1140 1 46.16350000 19.00850000 10.86200000 1157 | 1141 1 44.80575000 17.65075000 12.21975000 1158 | 1142 1 47.52125000 20.36625000 12.21975000 1159 | 1143 1 44.80575000 20.36625000 14.93525000 1160 | 1144 1 47.52125000 17.65075000 14.93525000 1161 | 1145 1 43.44800000 16.29300000 16.29300000 1162 | 1146 1 43.44800000 19.00850000 19.00850000 1163 | 1147 1 46.16350000 16.29300000 19.00850000 1164 | 1148 1 46.16350000 19.00850000 16.29300000 1165 | 1149 1 44.80575000 17.65075000 17.65075000 1166 | 1150 1 47.52125000 20.36625000 17.65075000 1167 | 1151 1 44.80575000 20.36625000 20.36625000 1168 | 1152 1 47.52125000 17.65075000 20.36625000 1169 | 1153 1 48.87900000 0.00000000 0.00000000 1170 | 1154 1 48.87900000 2.71550000 2.71550000 1171 | 1155 1 51.59450000 0.00000000 2.71550000 1172 | 1156 1 51.59450000 2.71550000 0.00000000 1173 | 1157 1 50.23675000 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1178 1 48.87900000 2.71550000 19.00850000 1195 | 1179 1 51.59450000 0.00000000 19.00850000 1196 | 1180 1 51.59450000 2.71550000 16.29300000 1197 | 1181 1 50.23675000 1.35775000 17.65075000 1198 | 1182 1 52.95225000 4.07325000 17.65075000 1199 | 1183 1 50.23675000 4.07325000 20.36625000 1200 | 1184 1 52.95225000 1.35775000 20.36625000 1201 | 1185 1 48.87900000 5.43100000 0.00000000 1202 | 1186 1 48.87900000 8.14650000 2.71550000 1203 | 1187 1 51.59450000 5.43100000 2.71550000 1204 | 1188 1 51.59450000 8.14650000 0.00000000 1205 | 1189 1 50.23675000 6.78875000 1.35775000 1206 | 1190 1 52.95225000 9.50425000 1.35775000 1207 | 1191 1 50.23675000 9.50425000 4.07325000 1208 | 1192 1 52.95225000 6.78875000 4.07325000 1209 | 1193 1 48.87900000 5.43100000 5.43100000 1210 | 1194 1 48.87900000 8.14650000 8.14650000 1211 | 1195 1 51.59450000 5.43100000 8.14650000 1212 | 1196 1 51.59450000 8.14650000 5.43100000 1213 | 1197 1 50.23675000 6.78875000 6.78875000 1214 | 1198 1 52.95225000 9.50425000 6.78875000 1215 | 1199 1 50.23675000 9.50425000 9.50425000 1216 | 1200 1 52.95225000 6.78875000 9.50425000 1217 | 1201 1 48.87900000 5.43100000 10.86200000 1218 | 1202 1 48.87900000 8.14650000 13.57750000 1219 | 1203 1 51.59450000 5.43100000 13.57750000 1220 | 1204 1 51.59450000 8.14650000 10.86200000 1221 | 1205 1 50.23675000 6.78875000 12.21975000 1222 | 1206 1 52.95225000 9.50425000 12.21975000 1223 | 1207 1 50.23675000 9.50425000 14.93525000 1224 | 1208 1 52.95225000 6.78875000 14.93525000 1225 | 1209 1 48.87900000 5.43100000 16.29300000 1226 | 1210 1 48.87900000 8.14650000 19.00850000 1227 | 1211 1 51.59450000 5.43100000 19.00850000 1228 | 1212 1 51.59450000 8.14650000 16.29300000 1229 | 1213 1 50.23675000 6.78875000 17.65075000 1230 | 1214 1 52.95225000 9.50425000 17.65075000 1231 | 1215 1 50.23675000 9.50425000 20.36625000 1232 | 1216 1 52.95225000 6.78875000 20.36625000 1233 | 1217 1 48.87900000 10.86200000 0.00000000 1234 | 1218 1 48.87900000 13.57750000 2.71550000 1235 | 1219 1 51.59450000 10.86200000 2.71550000 1236 | 1220 1 51.59450000 13.57750000 0.00000000 1237 | 1221 1 50.23675000 12.21975000 1.35775000 1238 | 1222 1 52.95225000 14.93525000 1.35775000 1239 | 1223 1 50.23675000 14.93525000 4.07325000 1240 | 1224 1 52.95225000 12.21975000 4.07325000 1241 | 1225 1 48.87900000 10.86200000 5.43100000 1242 | 1226 1 48.87900000 13.57750000 8.14650000 1243 | 1227 1 51.59450000 10.86200000 8.14650000 1244 | 1228 1 51.59450000 13.57750000 5.43100000 1245 | 1229 1 50.23675000 12.21975000 6.78875000 1246 | 1230 1 52.95225000 14.93525000 6.78875000 1247 | 1231 1 50.23675000 14.93525000 9.50425000 1248 | 1232 1 52.95225000 12.21975000 9.50425000 1249 | 1233 1 48.87900000 10.86200000 10.86200000 1250 | 1234 1 48.87900000 13.57750000 13.57750000 1251 | 1235 1 51.59450000 10.86200000 13.57750000 1252 | 1236 1 51.59450000 13.57750000 10.86200000 1253 | 1237 1 50.23675000 12.21975000 12.21975000 1254 | 1238 1 52.95225000 14.93525000 12.21975000 1255 | 1239 1 50.23675000 14.93525000 14.93525000 1256 | 1240 1 52.95225000 12.21975000 14.93525000 1257 | 1241 1 48.87900000 10.86200000 16.29300000 1258 | 1242 1 48.87900000 13.57750000 19.00850000 1259 | 1243 1 51.59450000 10.86200000 19.00850000 1260 | 1244 1 51.59450000 13.57750000 16.29300000 1261 | 1245 1 50.23675000 12.21975000 17.65075000 1262 | 1246 1 52.95225000 14.93525000 17.65075000 1263 | 1247 1 50.23675000 14.93525000 20.36625000 1264 | 1248 1 52.95225000 12.21975000 20.36625000 1265 | 1249 1 48.87900000 16.29300000 0.00000000 1266 | 1250 1 48.87900000 19.00850000 2.71550000 1267 | 1251 1 51.59450000 16.29300000 2.71550000 1268 | 1252 1 51.59450000 19.00850000 0.00000000 1269 | 1253 1 50.23675000 17.65075000 1.35775000 1270 | 1254 1 52.95225000 20.36625000 1.35775000 1271 | 1255 1 50.23675000 20.36625000 4.07325000 1272 | 1256 1 52.95225000 17.65075000 4.07325000 1273 | 1257 1 48.87900000 16.29300000 5.43100000 1274 | 1258 1 48.87900000 19.00850000 8.14650000 1275 | 1259 1 51.59450000 16.29300000 8.14650000 1276 | 1260 1 51.59450000 19.00850000 5.43100000 1277 | 1261 1 50.23675000 17.65075000 6.78875000 1278 | 1262 1 52.95225000 20.36625000 6.78875000 1279 | 1263 1 50.23675000 20.36625000 9.50425000 1280 | 1264 1 52.95225000 17.65075000 9.50425000 1281 | 1265 1 48.87900000 16.29300000 10.86200000 1282 | 1266 1 48.87900000 19.00850000 13.57750000 1283 | 1267 1 51.59450000 16.29300000 13.57750000 1284 | 1268 1 51.59450000 19.00850000 10.86200000 1285 | 1269 1 50.23675000 17.65075000 12.21975000 1286 | 1270 1 52.95225000 20.36625000 12.21975000 1287 | 1271 1 50.23675000 20.36625000 14.93525000 1288 | 1272 1 52.95225000 17.65075000 14.93525000 1289 | 1273 1 48.87900000 16.29300000 16.29300000 1290 | 1274 1 48.87900000 19.00850000 19.00850000 1291 | 1275 1 51.59450000 16.29300000 19.00850000 1292 | 1276 1 51.59450000 19.00850000 16.29300000 1293 | 1277 1 50.23675000 17.65075000 17.65075000 1294 | 1278 1 52.95225000 20.36625000 17.65075000 1295 | 1279 1 50.23675000 20.36625000 20.36625000 1296 | 1280 1 52.95225000 17.65075000 20.36625000 -------------------------------------------------------------------------------- /harmonic/subroutines.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | # -*- coding: utf-8 -*- 3 | """ 4 | Created on Mon Mar 11 10:36:56 2019 5 | 6 | @author: Ty Sterling 7 | ty.sterling@colorado.edu 8 | 9 | Another go at harmonic tr, bump hasn't gone away 10 | 11 | This script contains functions called by main 12 | """ 13 | 14 | import numpy as np 15 | import sys 16 | import scipy.linalg.blas as blas 17 | import scipy.sparse as sp 18 | 19 | ###################################################################### 20 | def makeTime(dt,tn): 21 | """ 22 | This function takes in the step size and number of steps in a block 23 | and returns the corresponding angular frequency and THz array 24 | """ 25 | om = np.arange(0,tn)*2*np.pi/(tn*dt) #angular frequency, positive val 26 | thz = om/2/np.pi*1e-12 #frequency in THz 27 | dom = om[1]-om[0] 28 | 29 | return [om, thz, dom] 30 | 31 | ######################################################################## 32 | def printParams(dtMD,dt,dT,steps,split,tn): 33 | """ 34 | Prints params to screen 35 | """ 36 | print(('\n\tUsing MD timestep:\t\t'+str(dtMD*1e12)+'\t\tps')) 37 | print(('\tEffective timestep:\t\t'+str(dt*1e12)+'\t\tps')) 38 | print(('\tTemperature bias:\t\t'+str(dT)+'\t\tK')) 39 | print(('\tTotal Number of Steps:\t\t'+str(steps)+'\t\t--')) 40 | print(('\tBlocks for averaging:\t\t'+str(split)+'\t\t--')) 41 | print(('\tTime per block:\t\t\t'+str(np.round(tn*dt*1e9,3))+'\t\tns')) 42 | print(('\tMaximum Frequency:\t\t'+str(np.round(0.5/dt*1e-12,3))+'\t\tTHz')) 43 | print(('\tFrequency Resolution:\t\t'+str(np.round(1/dt*1e-9/tn,3))+'\t\tMHz\n')) 44 | print('\t--------------------------------------------------------\n') 45 | 46 | ############################################################################ 47 | def gsmooth(Raw, win, dom): 48 | """ 49 | This function takes an numpy array defined over some domain and returns 50 | a gaussian smoothened version. "Raw" is the input numpy array. "win" is 51 | the width of the gaussian smoothing window used to initialize the 52 | smoothing window; e.g. if you have a signal from 0 to 20 THz and you want 53 | to smooth with a window of 1/3 THz, set "win = 1/3.0". dom is the constant 54 | spacing between values in the domain; e.g. if you have a numpy array, 55 | "freq", ranging from 0 to 20 THz and with length 10000, "dom = freq[1] - 56 | freq[0]" = 0.002 THz. If none of this makes sense, do like I did and 57 | figure it our yourself ;) 58 | """ 59 | 60 | gwin = round(win*1e12*2*np.pi/dom) #number of array elements in window 61 | if gwin % 2 == 0: #make sure its odd sized array 62 | gwin = gwin+1 63 | if gwin == 1: 64 | gauss = np.array([1]) #if array is size 1, convolve with self 65 | else: 66 | n = 2*np.arange(0,gwin)/(gwin-1)-(1) #centered at 0, sigma = 1 67 | n = (3*n) #set width of profile to 6*sigma i.e. end values ~= 0 68 | gauss = np.exp(-np.multiply(n,n)/2.0) #gaussian fx to convolve with 69 | gauss = gauss/np.sum(gauss) #normalized gaussian 70 | 71 | smooth = np.convolve(Raw,gauss,mode='same') 72 | return smooth 73 | 74 | 75 | ############################################################################ 76 | def readFij(infile): 77 | """ 78 | This function reads in the [dFi/duj] force constanst from 79 | LAMMPS compute commands. The structure of the infile should be blocks 80 | of data that are N atoms long. Here, N means the number of atoms in 81 | the interface region. Each atom of the N atoms in the block 82 | is the 'i' index in d^2Fi/duj. The LAMMPS code loops over all atoms j 83 | on the left side of the interface; j in the dFi/duj expression. There 84 | are NL = NR atoms on the left side of the inteface, i.e. the number on 85 | each side should (and MUST) be the same. Each atom on the left side, j, is 86 | looped over; in each loop iteration the atom is moved in the +x, then -x, 87 | then back to equilibrium. Then the atom is moved in the +y, then -y, then 88 | back to equilibrium. Finally, the atom is moved in the +z, then -z, then 89 | back to equilibrium. 90 | 91 | Thus, each line in each block in the file corresponds to an atom i. 92 | Each element in each line is the force felt by the atom in the x, y, and 93 | z direction (the force vector elements). For each block, the atom j is 94 | moved iteratively in the +x, then-x, then +y ... etc. 95 | 96 | The function returns kij, the matrix elements of the force constants 97 | between atoms on either side of the interface. 98 | kij has the shape [3*nr,3*nl] -> [dFi-x,y,z,duj-x,y,z]. Each individual 99 | force constant is defined as: 100 | 101 | dFi_a 102 | ---------- 103 | drj_b 104 | 105 | Which is interpreted as the change in force on atom i in the direction 106 | a = (x,y,z) due to the movement of atom j in b=(x,y,z). 107 | 108 | Each element of first dimension of the kij matrix corresponds to the 109 | force on atom i due to the movement of atom j in each direction 110 | 111 | dF1_x dF1_x dF1_x dF1_x 112 | ---------- ---------- ---------- ---------- ..... 113 | dr1_x dr1_y dr1_z dr2_x 114 | 115 | 116 | dF1_y dF1_y dF1_y dF1_y 117 | ---------- ---------- ---------- ---------- ..... 118 | dr1_x dr1_y dr1_z dr2_x 119 | 120 | 121 | dF1_z dF1_z dF1_z dF1_z 122 | ---------- ---------- ---------- ---------- ..... 123 | dr1_x dr1_y dr1_z dr2_x 124 | 125 | 126 | dF2_x dF2_x dF2_x dF2_x 127 | ---------- ---------- ---------- ---------- ..... 128 | dr1_x dr1_y dr1_z dr2_x 129 | 130 | : : : : 131 | : : : : 132 | """ 133 | with open(infile,'r') as fid: 134 | nl = int(fid.readline().strip().split()[1]) #number of atoms on left side 135 | nr = int(fid.readline().strip().split()[1]) #number of atoms on right side 136 | n = nl+nr #total number of atoms 137 | 138 | ids = np.zeros(n) #unique lammps ID 139 | side = np.zeros(n) #1 if on the left side, 2 if on the right 140 | for i in range(n): #read in the side data 141 | tmp = fid.readline().strip().split() 142 | ids[i] = int(tmp[0]) 143 | side[i] = int(tmp[1]) 144 | 145 | idsl = np.argwhere(side[:] == 1) #left ids 146 | idsr = np.argwhere(side[:] == 2) #left right 147 | 148 | if (nl != len(idsl) or nr != len(idsr) or nl != nr): 149 | sys.exit('\n\tLAMMPS SETUP ERROR: Number of atoms on left and ' 150 | 'right side don\'t match!\n') 151 | 152 | du = float(fid.readline().strip().split()[1]) #dr step size 153 | 154 | kii = np.zeros((nr*3,nl*3)) #force constants 155 | kij = np.zeros((nr*3,nl*3)) #force constants 156 | 157 | for i in range(nl*3): 158 | fplus = np.zeros((n,3)) # j in plus x,y,z 159 | fmin = np.zeros((n,3)) # j in minus x,y,z 160 | 161 | for j in range(9): #skip comments 162 | fid.readline() 163 | for j in range(n): #read force dF 164 | fplus[j,:] = fid.readline().strip().split()[1:4] 165 | 166 | for j in range(9): #skip comments 167 | fid.readline() 168 | for j in range(n): #read force dF 169 | fmin[j,:] = fid.readline().strip().split()[1:4] 170 | 171 | kii[:,i] = (fplus[idsl,:]-fmin[idsl,:]).reshape(nl*3) 172 | kij[:,i] = (fplus[idsr,:]-fmin[idsr,:]).reshape(nr*3) 173 | 174 | kii = -kii/(2*du) 175 | kij = -kij/(2*du) 176 | 177 | return [kij, du, idsl.reshape(nl), idsr.reshape(nr), ids, nl, nr, n] 178 | ########################################################################## 179 | 180 | 181 | 182 | ########################################################################## 183 | def computeQ(kij,vels,om,idsl,idsr,nl,nr,tn,dt,s): 184 | """ 185 | Compute the spectral heat current across the interface 186 | """ 187 | vfft = np.fft.fft(vels,axis=0)*dt 188 | 189 | qom = np.zeros(tn).astype(complex) 190 | vl = np.zeros((tn,nl*3)).astype(complex) 191 | vr = np.zeros((tn,nr*3)).astype(complex) 192 | 193 | vl[:,0::3] = vfft[:,idsl*3] 194 | vl[:,1::3] = vfft[:,idsl*3+1] 195 | vl[:,2::3] = vfft[:,idsl*3+2] 196 | vr[:,0::3] = vfft[:,idsr*3] 197 | vr[:,1::3] = vfft[:,idsr*3+1] 198 | vr[:,2::3] = vfft[:,idsr*3+2] 199 | 200 | # vl = np.asfortranarray(vl) 201 | # vr = np.asfortranarray(vr) 202 | # kij = np.asfortranarray(kij) 203 | 204 | kij = sp.csr_matrix(kij) 205 | vl = vl.T 206 | vr = vr.conj() 207 | 208 | print(('\n\tNow computing heat current for block '+str(s+1)+'\n')) 209 | num = tn//10 210 | for j in range(tn): 211 | if j != 0 and j%(num) == 0: #print progress updates 212 | print(('\t\tNow '+str(10*np.round(j/num,decimals=1))+ 213 | '% done computing heat current for block '+str(s+1))) 214 | if j == 0: 215 | qom[j] = 0+0j 216 | else: 217 | # qom[j] = -(blas.cgemm((1+0j),vr[j,None].conj(), 218 | # blas.cgemm((1+0j),kij,vl[j,None].T)))/om[j] 219 | qom[j] = -vr[j,:].dot(kij.dot(vl[:,j]))/om[j] 220 | 221 | return qom 222 | 223 | ############################################################################ 224 | def tic(): 225 | """ 226 | Same as MATLAB tic and toc functions. Use ty.tic() at the beginning of 227 | code you want to time and ty.toc() at the end. Once ty.toc() is reached, 228 | elapsted time will be printed to screen and optionally (by default) written 229 | to 'log.txt' file. 230 | """ 231 | import time 232 | global startTime_for_tictoc 233 | startTime_for_tictoc = time.time() 234 | 235 | def toc(): 236 | """ 237 | Same as MATLAB tic and toc functions. Use ty.tic() at the beginning of 238 | code you want to time and ty.toc() at the end. Once ty.toc() is reached, 239 | elapsted time will be printed to screen and optionally (by default) written 240 | to 'log.txt' file. 241 | """ 242 | import time 243 | if 'startTime_for_tictoc' in globals(): 244 | print(("\n\t\tElapsed time is "+ 245 | str(np.round(time.time()- 246 | startTime_for_tictoc,decimals=3))+" seconds.")) 247 | else: 248 | print("\n\t\tToc: start time not set") 249 | 250 | ############################################################################ 251 | def writeTr(outfile,thz,tr,qom,dT,dt,tn,win): 252 | "" 253 | "" 254 | with open(outfile, 'w') as fid: 255 | fid.write('delta T = '+str(dT)+' K\nMD timestep = '+str(dt)+' s\n' 256 | 'Gaussian window = '+str(win)+' THz\n-------\n') 257 | fid.write('THz tr qomRaw\n--------------------------------------\n') 258 | for i in range(tn-1): 259 | fid.write(str(thz[i])+'\t'+str(tr[i])+'\t'+str(qom[i])+'\n') 260 | fid.write(str(thz[-1])+'\t'+str(tr[-1])+'\t'+str(qom[-1])) 261 | 262 | 263 | 264 | ######################################################################### 265 | def readTr(infile): 266 | """ 267 | """ 268 | with open(infile, 'r') as fid: 269 | num_lines = sum(1 for line in fid)-6 #get number of line in file 270 | fid.seek(0) #return cursor to start of file 271 | 272 | for i in range(4): 273 | fid.readline() #skip comments 274 | 275 | columns = fid.readline().strip().split() 276 | ncol = len(columns) 277 | data = np.zeros((num_lines,ncol)) 278 | fid.readline() #skip comment 279 | 280 | for i in range(num_lines): 281 | tmp = fid.readline().strip().split() 282 | for j in range(ncol): 283 | data[i,j] = float(tmp[j]) 284 | 285 | return [data, columns] 286 | 287 | ########################################################################### 288 | def readVCM(infile): 289 | """ 290 | """ 291 | with open(infile, 'r') as fid: 292 | num_lines = sum(1 for line in fid)-3 #get number of line in file 293 | fid.seek(0) #return cursor to start of file 294 | 295 | for i in range(2): 296 | fid.readline() #skip comments 297 | col = fid.readline().strip().split()[2:] 298 | nrows = int(fid.readline().strip().split()[1]) 299 | ncol = len(col) 300 | ndat = int(num_lines/(1+nrows)) 301 | data = np.zeros((ndat,ncol)) 302 | 303 | line = 0 304 | fid.seek(0) #return cursor to start of file 305 | for i in range(3): 306 | fid.readline() #skip comments 307 | for i in range(ndat): 308 | fid.readline() #skip the timestep row 309 | for j in range(nrows): 310 | data[line,:] = fid.readline().strip().split()[1:] 311 | line = line+1 312 | 313 | return [data, col] --------------------------------------------------------------------------------