
From:  Nairhita Samanta 
Subject:  Re: [ESPResSousers] Doubt regarding integration steps 
Date:  Mon, 25 Apr 2016 11:38:06 +0530 
peterHope that helps,# let's make these small prime numbers, so that their product is unambiguousTry the following modification to your script:Hi Nairitha,each time step is $time_step long, each call co integrate executes $int_steps integration steps, and integrate is called $int_n_times times.
set int_n_times 3
set int_steps 7
set time_step 0.1000
thermostat langevin 1.0 1.0
setmd skin 0.400
setmd time_step $time_step
setmd time 0
# start main integration
for {set i 0} { $i < $int_n_times } {incr i} {
integrate $int_steps
}
set should_be [expr $int_n_times*$int_steps*$time_step];
set is [setmd time];
puts "is:$is, should_be: $should_be ratio:[expr $is/$should_be]"On Sat, Apr 23, 2016 at 3:53 PM, Nairhita Samanta <address@hidden> wrote:Hi Konard!
Thank you for your reply. I am still not very clear about it. Please see the following, that is the integration details in my script. Then where do I put the count which you have suggested? As I said I have two variables, in each $int_n_times the system is integrated by $int_steps*$dt.
for {set i 0} { $i < $int_n_times } {incr i} {
integrate $int_steps
integrate 0
incr j
}
}With regards,NairhitaOn Sat, Apr 23, 2016 at 6:38 PM, Konrad Breitsprecher <address@hidden> wrote:So the timestep is set bysetmd time_step $dtNow when you callintegrate $Nthe system is propagated by$N*$dt.The total elapsed simulation time is tracked internally, you get (or set) it via[setmd time]So a convenient way of handling time in Espresso is to callsetmd time 0before your integration loop and obtain the elapsed time also via [setmd time].You should also know the conversion to SI time. For example, if your units areLength: [Angstrom], Mass: [g/mol], Energy: [kJ/mol],then you elapsed time in SI units is [setmd time]*100 fs.Hope this helped,Regards,Konrad20160423 14:30 GMT+02:00 Nairhita Samanta <address@hidden>:Hello all!
I am little confused here understanding the timesteps of integration in Espresso. When we run a script, we generally have three parameters "time steps" (generally very small), "integration time" and "integration steps". Now while integrating, the system is being integrated "integration time" times and each of them has certain number of "integration steps" and and all the steps get integrated by dt="time steps".Now my question is if I want to report my simulations somewhere then what should be the total time of integration? Is it
("integration time" X "integration steps" X "time steps") in whatever is my unit system.I feel this is the most logical.Regards,Nairhitawww.natur.cuni.cz/chemistry/fyzchem/Přírodovědecká fakulta Univerzity Karlovy v PrazeKatedra fyzikální a makromolekulární chemieFaculty of Science, Charles University in Prague, Czech RepublicDr. Peter Košovan
Department of Physical and Macromolecular Chemistry
Tel. +420221951290Fax +420224919752
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