|
| From: | Georg Rempfer |
| Subject: | Re: [ESPResSo-users] questions about speed electrostatic on espresso |
| Date: | Wed, 18 May 2016 12:21:37 +0200 |
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
>
> ----------------------------------------------------------------------
> ## Initialization of random generator>
> 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
>
> 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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