Re: How to add a C code to NAMD properly?

From: Faramarz Joodaki (fjoodaki_at_my.uri.edu)
Date: Sun Dec 16 2018 - 11:50:41 CST

Dear Haochuan,

Thank you for your guidance!

Best Regards,
Faramarz

On Sat, Dec 15, 2018 at 8:33 PM <yjcoshc_at_gmail.com> wrote:

> Dear Faramarz,
>
> Please copy the email to the NAMD mailing list. This may give hints for
> other people who have the same question.
>
> As for your question, I am not very sure whether following code works:
>
> proc calc_funca {args} {
>
> set cartesian [lindex $args 0]
>
> set distance [lindex $args 1]
>
> }
>
> It may require some trying and debugging, but basically you can use puts
> to output the args to stdout and see the format of arguments from NAMD log.
>
> Thanks,
>
> Haochuan Chen
>
> 在 2018年12月15日 09:05, Faramarz Joodaki 写道:
>
> Dear Haochuan,
>
> Thanks again for your help! I have another question. I would be so
> grateful if you could guide me with this matter. How can I pass two or more
> parameters from colvars to the function in NAMD configuration file. For
> example:
>
> namespace eval funca { }
> proc calc_funca {arg1 arg2} {...}
>
>
> - arg1 can be cartesian coordinate
> - arg2 can be a distance
>
>
> Best Regards,
> Faramarz
>
> On Sat, Dec 8, 2018 at 1:28 PM Faramarz Joodaki <fjoodaki_at_my.uri.edu>
> wrote:
>
>> Dear Haochuan,
>>
>> Thank you very much for your complete explanation! So it seems that I
>> need to use TCL syntax for this kind of scripting.
>>
>> Best Regards,
>> Faramarz
>>
>> On Sat, Dec 8, 2018 at 6:55 AM <yjcoshc_at_gmail.com> wrote:
>>
>>> Hi Faramarz,
>>>
>>> In the NAMD configuration you can enable colvars and source this TCL
>>> script:
>>>
>>> namespace eval funca { }
>>> proc calc_funca {args} {
>>> puts $args
>>> set x0 [lindex [lindex $args 0] 0]
>>> set y0 [lindex [lindex $args 0] 1]
>>> set z0 [lindex [lindex $args 0] 2]
>>> return [expr $x0 + $y0 + $z0]
>>> }
>>>
>>> In the colvars file:
>>>
>>> colvar {
>>> name a
>>> scriptedFunction funca
>>>
>>> cartesian {
>>> atoms {atomNumbers {5}}
>>> }
>>> }
>>>
>>> Then the x, y and z coordinates of the atom 5 will be added up and
>>> outputted to the colvars trajectory file. A more comprehensive example is
>>> in https://github.com/Colvars/colvars/blob/master/colvartools/pathCV.tcl
>>>
>>> Regards,
>>>
>>> Haochuan Chen
>>>
>>> 在 2018年12月08日 10:56, Faramarz Joodaki 写道:
>>>
>>> Dear Haochuan,
>>>
>>> Thank you again for your great guidance! Since I am new in colvars and
>>> scriptedFunction. I would be so grateful if you could give me an example
>>> about this kind of scripting. For example, if we assume x, y, and z are
>>> atom coordinates, how can we write x+y+z code in this kind of scripting?
>>>
>>> Best Regards,
>>> Faramarz
>>>
>>> On Wed, Dec 5, 2018 at 8:51 PM Faramarz Joodaki <fjoodaki_at_my.uri.edu>
>>> wrote:
>>>
>>>> Dear Haochuan,
>>>>
>>>> Thank you for your guidance! I will try your method and if I have any
>>>> questions, I will ask you about that.
>>>>
>>>> Best Regards,
>>>> Faramarz
>>>>
>>>> > On Dec 5, 2018, at 8:45 PM, yjcoshc <yjcoshc_at_gmail.com> wrote:
>>>> >
>>>> > Haochuan
>>>>
>>>
>>>
>

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