# Question

Hello
I want to simulate solidification of nanoparticles during cooling, So i need to cool nanoparticles from high temperature to 0 K at a rate of 1 K/ 5ps, But i don`t know that how do it!!
How can i employ 1 K/ 5ps?

Hi Zahra,

The thermostats allow a smooth change of temperature (ramping) during a run by setting Tstart and Tstop to different values. Or you could impose many step-wise changes in temp by looping over an index-style variable.

Tim

Hello
I want to simulate solidification of nanoparticles during cooling, So i
need to cool nanoparticles from high temperature to 0 K at a rate of 1 K/
5ps, But i don`t know that how do it!!

all the thermostat fixes allow you to set a temperature ramp.

How can i employ 1 K/ 5ps?

you set the time step, you set how many steps you want to run, you set
the beginning and end of the temperature ramp. the rest is elementary
calculus.

axel.

axel.

This is the example.

timestep 1 (1fs)fix 1 all NVT or NPT temp 600.0 600.0 100.0
run 5000 (5ps associated with time step)

fix 1 all NVT or NPT temp 599.0 599.0 100.0
run 5000

fix 1 all NVT or NPT temp 598.0 598.0 100.0
run 5000

fix 1 all NVT or NPT temp 597.0 597.0 100.0
run 5000

fix 1 all NVT or NPT temp 596.0 596.0 100.0
run 5000

and so on

This is the rate of 1K/5ps as function of time step. If the time step is 1ps, run just 5 (run 5).

As Timothy Sirk mentioned, you can loop for this.

C.W.

This is the example.

NOOOOOooooooo!!!!!

tstart and tstop like tim mentioned.

I know it is a bad example. Simply say, I showed what the 1K/5ps means. The operation of the command is different.

I know it is a bad example. Simply say, I showed what the 1K/5ps means. The
operation of the command is different.

why not show a good example then??
it is so simple to do it right. that is why i didn't bother.

NO.

*because* it is so simple, there is *much* more value in going back to
the documentation and figuring it out for yourself.
i have given all the necessary pointers how you compute this. i think
that is something one can expect even from a beginner.

please remember that important part of learning is understanding the
process and not in having the answer.

axel.

OK. you do not have even an example. I got it.

He (Zahra) may understand a little bit more easily from my example than from your NO-example.

CW

OK. you do not have even an example. I got it.

He (Zahra) may understand a little bit more easily from my example than from

no. because it is a *bad* and incorrect example.

How do you verify the given example is bad or not without your GOOD example? Who knows? How do you know he may get some understanding from my bad example for the concept of 1K/5ps?

How do you verify the given example is bad or not without your GOOD example?

it has been mentioned multiple times to use Tstart and Tstop. that is
"the Right Way(tm)" to do a smooth temperature ramp.

Who knows? How do you know he may get some understanding from my bad example
for the concept of 1K/5ps?

your example does not do a 1K/5ps ramp. it shows 600x a 1K jump in the
target temperature. that is why it is a bad example.

axel.

> How do you verify the given example is bad or not without your GOOD
example?

it has been mentioned multiple times to use Tstart and Tstop. that is
"the Right Way(tm)" to do a smooth temperature ramp.

> Who knows? How do you know he may get some understanding from my bad
example
> for the concept of 1K/5ps?

your example does not do a 1K/5ps ramp. it shows 600x a 1K jump in the
target temperature. that is why it is a bad example.

The next line showed run 5ps at 599K and then run 5ps at 598K and run 5ps
at 597K....and so on. This is the rate of 1K/5ps from 600K to the lower
temperature. The concept is not wrong but the implementation is only dirty.

Therefore, show your example to verify your saying whether it is simple or
not. Nobody can believe whether your example is simple or not without a
SINGLE line example.

CW

[...]

your example does not do a 1K/5ps ramp. it shows 600x a 1K jump in the
target temperature. that is why it is a bad example.

The next line showed run 5ps at 599K and then run 5ps at 598K and run 5ps at
597K....and so on. This is the rate of 1K/5ps from 600K to the lower
temperature. The concept is not wrong but the implementation is only dirty.

i didn't say it is wrong, i said it is bad.

Therefore, show your example to verify your saying whether it is simple or
not. Nobody can believe whether your example is simple or not without a
SINGLE line example.

why don't you just do what i recommended zahra to do? you might learn
something as well.

axel

???

You definitely said “NOOOOOoooo”. Is this english word the same as WRONG? I did not give the exact solution for Zahra because of the same reason as you mentioned. He find a solution by himself with several trials and errors. I just simply expanded and explained with several lines for what the rate of 1K/5ps and hope him understand what the ramping is of 1K/5ps.

Am I still bad or wrong?

CW

???

You definitely said "NOOOOOoooo". Is this english word the same as WRONG?
I did not give the exact solution for Zahra because of the same reason
as you mentioned. He find a solution by himself with several trials and

no. that is where i vehemently disagree and that is where i said no in
this drastic fashion.
in my many years of teaching experience, the exact opposite is the case.

if i give people a bad example, they will keep using it however much
you explain that it is no good or that they should not use it, because
it is "a solution".

in fact, telling somebody that something must not be used for real,
usually has the opposite effect.

some random fragment of information that people find on the internet
without context, without references, from a person they know nothing
about, often seems to have more credit than a text book or a local
expert.

errors. I just simply expanded and explained with several lines for what the
rate of 1K/5ps and hope him understand what the ramping is of 1K/5ps.

Am I still bad or wrong?

why didn't you do as i recommended? you wasted a lot of everybody's time.
for the sake of your education and to stop wasting everybody's time,
here is what the manual suggests how you do a temperature ramp.

the proper example for the same case that you described would be (with
proper comments to explain the choices).

units real # set unit of time step to femtoseconds
timestep 1.0 # length of a timestep (= 1.0fs)

fix 1 all nvt temp 600.0 0.001 100.0 # it is not possible to
thermostat to exact zero. atoms cannot move at 0K.
run 3000000 # 5ps is 5000 timesteps.
=> 600K temperature ram to 0.0 at 1K/5ps require 600*5000 steps of 1
fs.

Now, you showed your simple example. Only three lines are needed to let him know. It is much simpler than write 12 back and forth emails. This is what the beginner wants (feeding them) even if they have to spend a lot of time for learning a new one.

I knew this is the proper way to use the fix command. However, your way to say judge other’s suggestions with simply saying “NOOOoooo” is not correct. That is very rude to others in the open mailing list which everyone uses.

Remember that this mailing-list is not only for you but also others. Please be kind to other. I am not blaming your knowledge but your attitude to others in the mailing list. If others are not correct in your manner, just neglect or be advising kindly.

CW

Now, you showed your simple example. Only three lines are needed to let him
know. It is much simpler than write 12 back and forth emails. This is what
the beginner wants (feeding them) even if they have to spend a lot of time
for learning a new one.

I knew this is the proper way to use the fix command. However, your way to
say judge other's suggestions with simply saying "NOOOoooo" is not correct.
That is very rude to others in the open mailing list which everyone uses.

if you knew what is the right answer, then why didn't *you* provide it
right away? that was your chance to be helpful and supportive. you
would have shut me up right away. rather you led me to believe that
you didn't know the answer either.

what is more rude? giving knowingly a bad example or telling somebody
where to find the right answer and not give the example?

Remember that this mailing-list is not only for you but also others. Please
be kind to other. I am not blaming your knowledge but your attitude to
others in the mailing list. If others are not correct in your manner, just

ok. so now you taught me a lesson. congratulations.

This is the open forum. I would not like to shut you up at all. Talk whatever you want but be generous.

Same thing. What I wrote is also a possible one of the examples for the beginners. The example could be a primitive example without loop or without ramping. Everyone instantly knows the repeated fix commands are not useful at all. Then, they will find the solution from what the ramping rate is from my example. Maybe not. I may be wrong at this point.

Remember that an example is not the solution but the one people may think then expand their knowledge.

In your point of view, it could be wrong. However, the example I wrote could be still useful to think of the temperature ramping. It is not useless at all.

I am really glad to teach you for the social manner.

You will be more generous than before in this mailing list.

Thanks.