Re: [ESPResSo-users] questions about speed electrostatic on espresso

[Kai Szuttor]

Your script works fine for me. The performance is about 650 integrations
per second for 180 particles. I dont have values to compare at hand but
this seems a reasonable speed for espresso.

Cheers,
Kai
On Tue, May 17, 2016 at 06:23:37PM +0000, ‪Zeinab Aghajani‬ ‪ wrote:
>    ----- Forwarded Message -----
>    From: a*-aZeinab Aghajania*NOT a*-a <address@hidden>
>    To: Georg Rempfer <address@hidden>
>    Sent: Saturday, 14 May 2016, 18:56:31
>    Subject: Re: [ESPResSo-users] questions about speed electrostatic on
>    espresso
>    Hi
>    I had asked a question about the runtime of my program befor.it's very
>    slow.I have attached an script including the particle placement and my
>    integration loop.My program is runing on a computer with below features.
>    OS  LINUX
>    RAM  6GB
>    Cache 6MB
>    HDD 1T
>    core i7 (1.8GHz)
>    I will be grateful if you check my program.
>    thanks a lot
> 
>      ----------------------------------------------------------------------
> 
>    From: Georg Rempfer <address@hidden>
>    To: address@hidden
>    Cc: "address@hidden" <address@hidden>
>    Sent: Friday, 13 May 2016, 13:56:21
>    Subject: Re: [ESPResSo-users] questions about speed electrostatic on
>    espresso
>    Please provide a complete simulation script, including particle placement
>    and your integration loop. These runtimes seem unusually high, indeed.
>    Greetings,
>    Georg
>    On Wed, May 11, 2016 at 10:52 AM, <address@hidden> wrote:
> 
>      Hi
>      I simulation a polymer with counterion in a box.
>      The size of simulation cell is Lx=5Rg   Ly=5Rg  Lz=10 Rg
>      Chain length is 46 and number of counterion is 138.
>      A  p3m algorithm is used to calculate the full electrostatic
>      interactions between charged momomer and counterions.q_momomer =-3
>       q_counterin =+1 for 3000 step it takes about 50 minute.It is very
>      slow.How do i improve it?
>      parametrs:
>      time_step 0.01
>      skin 0.4
>      lj_sigma 1.0
>       lj_epsilon 1.0
>       bjerrum [expr 0.7 * $lj_sigma]
>      d_mon $lj_sigma
>       d_ion [expr 0.425*$lj_sigma]
>       monomer_momomer_epsilon $lj_epsilon
>       monomer_momomer_sigma $d_mon
>      monomer_momomer_cutoff [expr $monomer_momomer_sigma * pow(2.0,1./6.)]
>       monomer_momomer_shift [calc_lj_shift $monomer_momomer_sigma
>      $monomer_momomer_cutoff]
>       monomer_momomer_offset 0.0
>       monomer_ion_epsilon $lj_epsilon
>       monomer_ion_sigma [expr ($d_mon+$d_ion)/2.0]
>       monomer_ion_cutoff [expr $monomer_ion_sigma * pow(2.0,1./6.)]
>       monomer_ion_shift [calc_lj_shift $monomer_ion_sigma
>      $monomer_ion_cutoff]
>       monomer_ion_offset 0.0
>       ion_ion_epsilon $lj_epsilon
>       ion_ion_sigma $d_ion
>       ion_ion_cutoff [expr $ion_ion_sigma * pow(2.0,1./6.)]
>       ion_ion_shift [calc_lj_shift $ion_ion_sigma $ion_ion_cutoff]
>       ion_ion_offset 0.0
>      bond_K 30.
>       bond_rcut [expr 1.2 * $lj_sigma]
>      temperature 1.0
>       gamma 15.34
>      interacyions:
>      inter 0 fene $bond_K $bond_rcut
>      inter 0 0 lennard-jones $monomer_momomer_epsilon $monomer_momomer_sigma
>      $monomer_momomer_cutoff $monomer_momomer_shift $monomer_momomer_offset
>      inter 0 1 lennard-jones $monomer_ion_epsilon $monomer_ion_sigma
>      $monomer_ion_cutoff $monomer_ion_shift $monomer_ion_offset
>      inter 1 1 lennard-jones $ion_ion_epsilon $ion_ion_sigma $ion_ion_cutoff
>      $ion_ion_shift $ion_ion_offset
>      inter coulomb $bjerrum p3m tune accuracy 1e-3
>      Thanks

> 
> ## Initialization of random generator
> set init_seed [clock clicks]
> append seeds $init_seed
> t_random seed [expr {int(rand()*10000)}] [expr {int(rand()*10000)}] [expr 
> {int(rand()*10000)}] [expr {int(rand()*10000)}]
> puts "$init_seed"
> 
> puts "Program Information: \n[code_info]\n"
> 
> ## MD parameters
> setmd time_step 0.01
> ### these tune the speed
> #setmd max_num_cells 1000
> setmd skin 0.4
> 
> set grid_size 1.0
> 
> # particle parameters
> set num_polymers 1
> set num_monomers_per_polymer 45
> puts "number of monomers is $num_monomers_per_polymer"
> 
> # interaction parameters
> set lj_sigma 1.0
> set lj_epsilon 1.0
> set bjerrum [expr 0.7 * $lj_sigma]
> 
> set q_mon 3.0
> set q_ion 1.0
> 
> set d_mon $lj_sigma
> set d_ion [expr 0.425*$lj_sigma]
> 
> set monomer_momomer_epsilon $lj_epsilon
> set monomer_momomer_sigma $d_mon
> set monomer_momomer_cutoff [expr $monomer_momomer_sigma * pow(2.0,1./6.)]
> set monomer_momomer_shift [calc_lj_shift $monomer_momomer_sigma 
> $monomer_momomer_cutoff]
> set monomer_momomer_offset 0.0
> 
> set monomer_ion_epsilon $lj_epsilon
> set monomer_ion_sigma [expr ($d_mon+$d_ion)/2.0]
> set monomer_ion_cutoff [expr $monomer_ion_sigma * pow(2.0,1./6.)]
> set monomer_ion_shift [calc_lj_shift $monomer_ion_sigma $monomer_ion_cutoff]
> set monomer_ion_offset 0.0
> 
> set ion_ion_epsilon $lj_epsilon
> set ion_ion_sigma $d_ion
> set ion_ion_cutoff [expr $ion_ion_sigma * pow(2.0,1./6.)]
> set ion_ion_shift [calc_lj_shift $ion_ion_sigma $ion_ion_cutoff]
> set ion_ion_offset 0.0
> 
> set bond_K 30.
> set bond_rcut [expr 1.2 * $lj_sigma]
> set temperature 1.0
> 
> set gamma 15.34
> ## Information of steps
> set init_num_step [expr int(1500*sqrt($num_monomers_per_polymer/10))]
> set init_internal_step 500
> 
> ## Set the box size
> 
> set box_l [expr $lj_sigma * int(pow($num_monomers_per_polymer / 10. * 
> pow(15.0,3.),1./3.))]
> set Rc [expr 
> 1.7*$lj_sigma*sqrt($num_monomers_per_polymer)*10/12.*9/(0.7*5*$lj_sigma)]
> ## Box size
> set box_lx [expr int(($box_l/2. + 4*$lj_sigma + $Rc + 5 + 
> $box_l/2.)/$grid_size)*$grid_size]
> set box_ly [expr int($box_l/$grid_size)*$grid_size]
> set box_lz [expr int($box_l/$grid_size)*$grid_size]
> 
> setmd box_l $box_lx $box_ly $box_lz
> 
> ## position for centermass of polymer
> set x_0       [expr $box_l/2. + 4*$lj_sigma + $Rc + 5/2.]
> set y_0       [expr $box_ly / 2.]
> set z_0       [expr $box_lz / 2.]
> ##Boundary conditions for set up conterion
> set wall1 [expr $x_0 - 5/2 - $lj_sigma]
> set wall2 [expr $x_0 + 5/2 + $lj_sigma]
> 
> ## SET UP THE INTERACTIONS
> 
> inter 0 fene $bond_K $bond_rcut
> inter 0 0 lennard-jones $monomer_momomer_epsilon $monomer_momomer_sigma 
> $monomer_momomer_cutoff $monomer_momomer_shift $monomer_momomer_offset
> inter 0 1 lennard-jones $monomer_ion_epsilon $monomer_ion_sigma 
> $monomer_ion_cutoff $monomer_ion_shift $monomer_ion_offset
> inter 1 1 lennard-jones $ion_ion_epsilon $ion_ion_sigma $ion_ion_cutoff 
> $ion_ion_shift $ion_ion_offset
> 
> set vtf_output "yes"
> 
>   #############################################################
>   # SET UP THE SYSTEM
> 
>   setmd time 0.0
> 
>   set x0 [expr $x_0 - 5/2.0 - $Rc]
>   set y0 [expr $y_0]
>   set z0 [expr $z_0]
> 
>   polymer $num_polymers $num_monomers_per_polymer $d_mon pos $x0 $y0 $z0 type 
> 0 bond 0
> 
>   set px [lindex [part [expr $num_monomers_per_polymer/2] print pos] 0]
>   set py [lindex [part [expr $num_monomers_per_polymer/2] print pos] 1]
>   set pz [lindex [part [expr $num_monomers_per_polymer/2] print pos] 2]
> 
>   set distx [expr $x0-$px]
>   set disty [expr $y0-$py]
>   set distz [expr $z0-$pz]
> 
>   for { set i 0 } { $i < [setmd n_part]} { incr i } {
>     set posx [lindex [part $i print pos] 0]
>     set posy [lindex [part $i print pos] 1]
>     set posz [lindex [part $i print pos] 2]
>     set typ [part $i print type] 
>     part $i pos [expr $posx + $distx] [expr $posy + $disty] [expr $posz + 
> $distz] type $typ q 0
>     puts "$i [part $i print pos type q]"
>   }
>  
>     for { set i 0 } { $i < $num_monomers_per_polymer } {incr i} {
>       part $i q [expr -$q_mon]
>   }
>     set num_counterion [expr 
> int($num_polymers*$num_monomers_per_polymer*$q_mon/$q_ion)]
>     set min_init_dist [analyze mindist]
>     for {set i $num_monomers_per_polymer} { $i < [expr $num_counterion + 
> $num_monomers_per_polymer] } {incr i} {
>       set flag 0
>       while {$flag != 1} {
>         set posx [expr $wall1*[t_random]]
>         set posy [expr $box_ly*[t_random]]
>         set posz [expr $box_lz*[t_random]]
>         set flag 1
>         set dist 1000
>         part $i pos $posx $posy $posz type 1 q $q_ion
>         set dist [analyze mindist]
>         if ($dist<$min_init_dist) {
>           set flag 0
>         }
>       }
>       puts "$i [part $i print pos type q] [setmd n_part] [analyze mindist] 
> $dist"
>     }
>   ##############################################################
> 
>  
>   # open VTF file
>   set pre_vtf_file [open "pos.vtf" "w"]
>   writevsf $pre_vtf_file
>   writevcf $pre_vtf_file
>   flush $pre_vtf_file
> 
>   #############################################################
>   # SETTING UP THE THERMOSTAT
> 
> 
>   thermostat langevin $temperature $gamma
>    
>   
>   part [expr $num_monomers_per_polymer/2] fix
> 
>   #############################################################
>   # WARMUP INTEGRATION
>   puts "\nWarmup:"
> 
>   # after warmup, all particle pairs should have at least this distance
>   set min_dist [expr 0.85 * $lj_sigma]
> 
>   # compute the minimal distance between two particles
>   set act_min_dist [analyze mindist]
>   puts "$act_min_dist"
> 
>   # set LJ capping
>   set cap 20
>   inter ljforcecap $cap
> 
>   for {set i 0} { $act_min_dist < $min_dist } {incr i} {
>       integrate 100
> 
>       # Warmup criterion
>       set act_min_dist [analyze mindist]
>       puts "\tstep=$i, cap=$cap, act_min_dist = $act_min_dist"
> 
>       # Increase LJ cap
>       set cap [expr $cap+10]
>       inter ljforcecap $cap
>   }
> 
>   # turn off capping
>   inter ljforcecap 0
> 
>   #############################################################
>   # TURNING ON ELECTROSTATIC FORCE
> 
>     puts [inter coulomb $bjerrum p3m tune accuracy 1e-3]
>  
> 
>   #############################################################
>   # EQUILLIBRATION INTEGRATION
> set start [clock clicks -milliseconds]
>   for { set i 0 } { $i < $init_num_step } { incr i } {
> 
>     integrate $init_internal_step
> 
>     if { $i%50==0 } {
>       writevcf $pre_vtf_file
>       flush $pre_vtf_file
>     }
>    puts "$i"
>     }
>     
>   set last [clock clicks -milliseconds]
>  set time_taken [expr $last-$start]
> puts "$time_taken"

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