espressomd-users
[Top][All Lists]
Advanced

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [ESPResSo-users] Espressomd-users Digest, Vol 104, Issue 2


From: Raghvendra Singh
Subject: Re: [ESPResSo-users] Espressomd-users Digest, Vol 104, Issue 2
Date: Fri, 6 Sep 2019 13:38:14 +0200 (CEST)

Hi Kai,
I am using the latest version of espresso (espresso-4.0.2).
I went through the documentation and tried to implement the output directives 
as you can see from the script I posted but I just get one initial frame 
nothing else no logs either.

best
Raghav

----- Original Message -----
From: address@hidden
To: "espressomd-users" <address@hidden>
Sent: Friday, September 6, 2019 1:15:33 PM
Subject: Espressomd-users Digest, Vol 104, Issue 2

Send Espressomd-users mailing list submissions to
        address@hidden

To subscribe or unsubscribe via the World Wide Web, visit
        https://lists.nongnu.org/mailman/listinfo/espressomd-users
or, via email, send a message with subject or body 'help' to
        address@hidden

You can reach the person managing the list at
        address@hidden

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Espressomd-users digest..."


Today's Topics:

   1. writing log and trajectories (Raghvendra Singh)
   2. Re: writing log and trajectories (Kai Szuttor)


----------------------------------------------------------------------

Message: 1
Date: Fri, 6 Sep 2019 13:03:31 +0200 (CEST)
From: Raghvendra Singh <address@hidden>
To: address@hidden
Subject: [ESPResSo-users] writing log and trajectories
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset=utf-8

Hello All, 

I am newbie to EspressoMD and in a testing trial phase of it.
I am trying to run a simple LJ simulation with multispecies simulation system.

There is a problem with writing appropriate log and trajectory for my 
simulation.
I went through the mailing list archive and documentation and still find it 
hard to manage what I want.

this is a script I am using to run the simulation, please help me out with 
getting the appropriate outputs required for further analysis. 
I would to have an output log and a trajectory every 100 step.

Thank you all

Best
Raghav
#########################################################################################################################################
import espressomd
import MDAnalysis as mda
from espressomd.visualization_opengl import openGLLive
from espressomd import electrostatics
from espressomd.io.writer import vtf
from espressomd import MDA_ESP
import numpy as np

required_features = ["P3M", "LENNARD_JONES", "MASS"]
espressomd.assert_features(required_features)

box = [200, 200, 200]
system = espressomd.System(box_l=box)

fp=open('trajectory.vtf', mode='w+t')

system.cell_system.set_domain_decomposition(use_verlet_lists=True)
#visualizer = openGLLive(system, background_color=[1, 1, 1],
                        drag_enabled=True, drag_force=10)

system.set_random_state_PRNG()
system.seed=42
# TIMESTEP
time_step_fs = 1.0
system.time_step = time_step_fs * 1.0e-2
system.cell_system.skin = 1.2

# TEMPERATURE
SI_temperature = 300.0
kb_kjmol = 0.0083145
temperature = SI_temperature * kb_kjmol

# COULOMB PREFACTOR (elementary charge)^2 / (4*pi*epsilon_0) in Angstrom *
# kJ/mol
epsilon_r = 4.0
coulomb_prefactor = 1.67101e5 * kb_kjmol / epsilon_r

# FORCE FIELDS
species = ["Cl", "Na", "C1", "C2","C3","C4","CCP","Solvent"]
types = {"Cl": 0, "Na": 1, "C1": 2,"C2":3,"C3":4,"C4":5,"CCP":6,"Solvent":7}
charges = {"Cl": -1.0, "Na": 1.0, "C1": -6.0, "C2": 0.0, "C3": 0.0, "C4": 
0.0,"CCP":6,"Solvent": 0.0}
lj_sigmas = {"Cl": 3.85, "Na": 2.52, "C1": 10.0, "C2": 10.0, "C3": 10.0, "C4": 
10.0,"CCP":5, "Solvent": 1.5}
lj_epsilons = {"Cl": 192.45, "Na": 17.44,
               "C1": 100.0, "C2": 100.0,
               "C3": 100.0, "C4": 100.0,
               "CCP": 70, "Solvent": 50.0}
lj_cuts = {"Cl": 2.0 * lj_sigmas["Cl"], "Na": 2.0 * lj_sigmas["Na"],
           "C1": 5.0 * lj_sigmas["C1"],"C2": 5.0 * lj_sigmas["C2"],
           "C3": 5.0 * lj_sigmas["C3"],"C4": 5.0 * lj_sigmas["C4"],
           "CCP": 2.5 * lj_sigmas["CCP"],"Solvent": 2.0 * lj_sigmas["Solvent"]}
masses = {"Cl": 35.453, "Na": 22.99, "C1": 100, "C2": 100, "C3": 100, "C4": 
100,"CCP": 50, "Solvent": 18.0}

n_ionpairs = 150
for i in range(n_ionpairs):
    for t in ["Na", "Cl"]:
        system.part.add(pos=box * np.random.random(3),
                        q=charges[t], type=types[t], mass=masses[t])

n_colloids = 150
t = "C1"
t_co = "Cl"
for i in range(n_colloids):
    system.part.add(pos=box * np.random.random(3),
                    q=charges[t], type=types[t], mass=masses[t])
    for i in range(int(abs(charges[t]))):
        system.part.add(pos=box * np.random.random(3),
                        q=charges[t_co], type=types[t_co], mass=masses[t_co])

n_colloids = 150
t = "C2"
t_co = "Na"
for i in range(n_colloids):
    system.part.add(pos=box * np.random.random(3),
                    q=charges[t], type=types[t], mass=masses[t])
    for i in range(int(abs(charges[t]))):
        system.part.add(pos=box * np.random.random(3),
                        q=charges[t_co], type=types[t_co], mass=masses[t_co])

n_colloids = 150
t = "C3"
t_co = "Cl"
for i in range(n_colloids):
    system.part.add(pos=box * np.random.random(3),
                    q=charges[t], type=types[t], mass=masses[t])
    for i in range(int(abs(charges[t]))):
        system.part.add(pos=box * np.random.random(3),
                        q=charges[t_co], type=types[t_co], mass=masses[t_co])

n_colloids = 150
t = "C4"
t_co = "Cl"
for i in range(n_colloids):
    system.part.add(pos=box * np.random.random(3),
                    q=charges[t], type=types[t], mass=masses[t])
    for i in range(int(abs(charges[t]))):
        system.part.add(pos=box * np.random.random(3),
                        q=charges[t_co], type=types[t_co], mass=masses[t_co])

n_colloids = 150
t = "CCP"
t_co = "Na"
for i in range(n_colloids):
    system.part.add(pos=box * np.random.random(3),
                    q=charges[t], type=types[t], mass=masses[t])
    for i in range(int(abs(charges[t]))):
        system.part.add(pos=box * np.random.random(3),
                        q=charges[t_co], type=types[t_co], mass=masses[t_co])

n_solvents = 0
t = "Solvent"
for i in range(n_solvents):
    system.part.add(pos=box * np.random.random(3),
                    q=charges[t], type=types[t], mass=masses[t])


def combination_rule_epsilon(rule, eps1, eps2):
    if rule == "Lorentz":
        return (eps1 * eps2)**0.5
    else:
        return ValueError("No combination rule defined")


def combination_rule_sigma(rule, sig1, sig2):
    if rule == "Berthelot":
        return (sig1 + sig2) * 0.5
    else:
        return ValueError("No combination rule defined")


# Lennard-Jones interactions parameters
for i in range(len(species)):
    for j in range(i, len(species)):
        s = [species[i], species[j]]
        lj_sig = combination_rule_sigma(
            "Berthelot", lj_sigmas[s[0]], lj_sigmas[s[1]])
        lj_cut = combination_rule_sigma(
            "Berthelot", lj_cuts[s[0]], lj_cuts[s[1]])
        lj_eps = combination_rule_epsilon(
            "Lorentz", lj_epsilons[s[0]], lj_epsilons[s[1]])

        system.non_bonded_inter[types[s[0]], 
types[s[1]]].lennard_jones.set_params(
            epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, shift="auto")

energy = system.analysis.energy()
print("Before Minimization: E_total = {}".format(energy['total']))
system.minimize_energy.init(f_max=1000, gamma=30.0,
                            max_steps=10000, max_displacement=0.01)
system.minimize_energy.minimize()
energy = system.analysis.energy()
print("After Minimization: E_total = {}".format(energy['total']))

print("Tune p3m")
p3m = electrostatics.P3M(prefactor=coulomb_prefactor, accuracy=1e-1)
system.actors.add(p3m)

system.thermostat.set_langevin(kT=temperature, gamma=2.0)

vtf.writevsf(system, fp, types='all')
vtf.writevcf(system, fp, types='all')
for n in num_steps:
    system.integrator.run(100)
    vtf.writevcf(system, fp)
fp.close()
vtf.writevsf(system, fp, types='all')
#########################################################################################################################################



------------------------------

Message: 2
Date: Fri, 6 Sep 2019 13:15:11 +0200
From: Kai Szuttor <address@hidden>
To: Raghvendra Singh <address@hidden>
Cc: address@hidden
Subject: Re: [ESPResSo-users] writing log and trajectories
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset="utf-8"

Hi,

could you please tell us which version of ESPReSso you are using?
If you are using the current release, find documentation for file I/O here: 
http://espressomd.org/html/doc4.0.2/io.html 
<http://espressomd.org/html/doc4.0.2/io.html>

Best,

Kai


Kai Szuttor
Institute for Computational Physics
Universit├Ąt Stuttgart
Allmandring 3
Room 1.084
70569 Stuttgart, Germany
Phone: +49 711 685-67707

> On 6. Sep 2019, at 13:03, Raghvendra Singh <address@hidden> wrote:
> 
> Hello All, 
> 
> I am newbie to EspressoMD and in a testing trial phase of it.
> I am trying to run a simple LJ simulation with multispecies simulation system.
> 
> There is a problem with writing appropriate log and trajectory for my 
> simulation.
> I went through the mailing list archive and documentation and still find it 
> hard to manage what I want.
> 
> this is a script I am using to run the simulation, please help me out with 
> getting the appropriate outputs required for further analysis. 
> I would to have an output log and a trajectory every 100 step.
> 
> Thank you all
> 
> Best
> Raghav
> #########################################################################################################################################
> import espressomd
> import MDAnalysis as mda
> from espressomd.visualization_opengl import openGLLive
> from espressomd import electrostatics
> from espressomd.io.writer import vtf
> from espressomd import MDA_ESP
> import numpy as np
> 
> required_features = ["P3M", "LENNARD_JONES", "MASS"]
> espressomd.assert_features(required_features)
> 
> box = [200, 200, 200]
> system = espressomd.System(box_l=box)
> 
> fp=open('trajectory.vtf', mode='w+t')
> 
> system.cell_system.set_domain_decomposition(use_verlet_lists=True)
> #visualizer = openGLLive(system, background_color=[1, 1, 1],
>                        drag_enabled=True, drag_force=10)
> 
> system.set_random_state_PRNG()
> system.seed=42
> # TIMESTEP
> time_step_fs = 1.0
> system.time_step = time_step_fs * 1.0e-2
> system.cell_system.skin = 1.2
> 
> # TEMPERATURE
> SI_temperature = 300.0
> kb_kjmol = 0.0083145
> temperature = SI_temperature * kb_kjmol
> 
> # COULOMB PREFACTOR (elementary charge)^2 / (4*pi*epsilon_0) in Angstrom *
> # kJ/mol
> epsilon_r = 4.0
> coulomb_prefactor = 1.67101e5 * kb_kjmol / epsilon_r
> 
> # FORCE FIELDS
> species = ["Cl", "Na", "C1", "C2","C3","C4","CCP","Solvent"]
> types = {"Cl": 0, "Na": 1, "C1": 2,"C2":3,"C3":4,"C4":5,"CCP":6,"Solvent":7}
> charges = {"Cl": -1.0, "Na": 1.0, "C1": -6.0, "C2": 0.0, "C3": 0.0, "C4": 
> 0.0,"CCP":6,"Solvent": 0.0}
> lj_sigmas = {"Cl": 3.85, "Na": 2.52, "C1": 10.0, "C2": 10.0, "C3": 10.0, 
> "C4": 10.0,"CCP":5, "Solvent": 1.5}
> lj_epsilons = {"Cl": 192.45, "Na": 17.44,
>               "C1": 100.0, "C2": 100.0,
>               "C3": 100.0, "C4": 100.0,
>               "CCP": 70, "Solvent": 50.0}
> lj_cuts = {"Cl": 2.0 * lj_sigmas["Cl"], "Na": 2.0 * lj_sigmas["Na"],
>           "C1": 5.0 * lj_sigmas["C1"],"C2": 5.0 * lj_sigmas["C2"],
>           "C3": 5.0 * lj_sigmas["C3"],"C4": 5.0 * lj_sigmas["C4"],
>           "CCP": 2.5 * lj_sigmas["CCP"],"Solvent": 2.0 * lj_sigmas["Solvent"]}
> masses = {"Cl": 35.453, "Na": 22.99, "C1": 100, "C2": 100, "C3": 100, "C4": 
> 100,"CCP": 50, "Solvent": 18.0}
> 
> n_ionpairs = 150
> for i in range(n_ionpairs):
>    for t in ["Na", "Cl"]:
>        system.part.add(pos=box * np.random.random(3),
>                        q=charges[t], type=types[t], mass=masses[t])
> 
> n_colloids = 150
> t = "C1"
> t_co = "Cl"
> for i in range(n_colloids):
>    system.part.add(pos=box * np.random.random(3),
>                    q=charges[t], type=types[t], mass=masses[t])
>    for i in range(int(abs(charges[t]))):
>        system.part.add(pos=box * np.random.random(3),
>                        q=charges[t_co], type=types[t_co], mass=masses[t_co])
> 
> n_colloids = 150
> t = "C2"
> t_co = "Na"
> for i in range(n_colloids):
>    system.part.add(pos=box * np.random.random(3),
>                    q=charges[t], type=types[t], mass=masses[t])
>    for i in range(int(abs(charges[t]))):
>        system.part.add(pos=box * np.random.random(3),
>                        q=charges[t_co], type=types[t_co], mass=masses[t_co])
> 
> n_colloids = 150
> t = "C3"
> t_co = "Cl"
> for i in range(n_colloids):
>    system.part.add(pos=box * np.random.random(3),
>                    q=charges[t], type=types[t], mass=masses[t])
>    for i in range(int(abs(charges[t]))):
>        system.part.add(pos=box * np.random.random(3),
>                        q=charges[t_co], type=types[t_co], mass=masses[t_co])
> 
> n_colloids = 150
> t = "C4"
> t_co = "Cl"
> for i in range(n_colloids):
>    system.part.add(pos=box * np.random.random(3),
>                    q=charges[t], type=types[t], mass=masses[t])
>    for i in range(int(abs(charges[t]))):
>        system.part.add(pos=box * np.random.random(3),
>                        q=charges[t_co], type=types[t_co], mass=masses[t_co])
> 
> n_colloids = 150
> t = "CCP"
> t_co = "Na"
> for i in range(n_colloids):
>    system.part.add(pos=box * np.random.random(3),
>                    q=charges[t], type=types[t], mass=masses[t])
>    for i in range(int(abs(charges[t]))):
>        system.part.add(pos=box * np.random.random(3),
>                        q=charges[t_co], type=types[t_co], mass=masses[t_co])
> 
> n_solvents = 0
> t = "Solvent"
> for i in range(n_solvents):
>    system.part.add(pos=box * np.random.random(3),
>                    q=charges[t], type=types[t], mass=masses[t])
> 
> 
> def combination_rule_epsilon(rule, eps1, eps2):
>    if rule == "Lorentz":
>        return (eps1 * eps2)**0.5
>    else:
>        return ValueError("No combination rule defined")
> 
> 
> def combination_rule_sigma(rule, sig1, sig2):
>    if rule == "Berthelot":
>        return (sig1 + sig2) * 0.5
>    else:
>        return ValueError("No combination rule defined")
> 
> 
> # Lennard-Jones interactions parameters
> for i in range(len(species)):
>    for j in range(i, len(species)):
>        s = [species[i], species[j]]
>        lj_sig = combination_rule_sigma(
>            "Berthelot", lj_sigmas[s[0]], lj_sigmas[s[1]])
>        lj_cut = combination_rule_sigma(
>            "Berthelot", lj_cuts[s[0]], lj_cuts[s[1]])
>        lj_eps = combination_rule_epsilon(
>            "Lorentz", lj_epsilons[s[0]], lj_epsilons[s[1]])
> 
>        system.non_bonded_inter[types[s[0]], 
> types[s[1]]].lennard_jones.set_params(
>            epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, shift="auto")
> 
> energy = system.analysis.energy()
> print("Before Minimization: E_total = {}".format(energy['total']))
> system.minimize_energy.init(f_max=1000, gamma=30.0,
>                            max_steps=10000, max_displacement=0.01)
> system.minimize_energy.minimize()
> energy = system.analysis.energy()
> print("After Minimization: E_total = {}".format(energy['total']))
> 
> print("Tune p3m")
> p3m = electrostatics.P3M(prefactor=coulomb_prefactor, accuracy=1e-1)
> system.actors.add(p3m)
> 
> system.thermostat.set_langevin(kT=temperature, gamma=2.0)
> 
> vtf.writevsf(system, fp, types='all')
> vtf.writevcf(system, fp, types='all')
> for n in num_steps:
>    system.integrator.run(100)
>    vtf.writevcf(system, fp)
> fp.close()
> vtf.writevsf(system, fp, types='all')
> #########################################################################################################################################

-------------- next part --------------
An HTML attachment was scrubbed...
URL: 
<https://lists.nongnu.org/archive/html/espressomd-users/attachments/20190906/fd6ab100/attachment.html>

------------------------------

Subject: Digest Footer

_______________________________________________
Espressomd-users mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/espressomd-users


------------------------------

End of Espressomd-users Digest, Vol 104, Issue 2
************************************************



reply via email to

[Prev in Thread] Current Thread [Next in Thread]