Dear all,
All the variables in my program is private. After I add it into Amber, why
are there so many variables in Amber source codes are ambiguous
reference?Such as :
>In file _egb.f:436
> integer iac,ico,numex,natex,ntypes,natom,natbel,ncopy
> 1
> Error: Name 'ntypes' at (1) is an ambiguous reference to 'ntypes' from
> current program unit
> In file _egb.f:639
>
> ico(*),numex(*),natex(*),fs(*),reff(natom), onereff(natom), &
> 1
> Error: Name 'natom' at (1) is an ambiguous reference to 'natom' from
> current program unit
> In file _egb.f:687
>
> charge(qmmm_nml%iqmatoms(qm_temp_count)) = &
> 1
> Error: Unclassifiable statement at (1)
Thanks a lot,
Xin
On Wed, 16 May 2012 10:04:12 -0700, Xin Geng <xingeng2011.berkeley.edu>
wrote:
> After I "make depend", lots of errors appear as follows:
>
> In file _egb.f:436
>
> integer iac,ico,numex,natex,ntypes,natom,natbel,ncopy
> 1
> Error: Name 'ntypes' at (1) is an ambiguous reference to 'ntypes' from
> current program unit
> In file _egb.f:639
>
> ico(*),numex(*),natex(*),fs(*),reff(natom), onereff(natom), &
> 1
> Error: Name 'natom' at (1) is an ambiguous reference to 'natom' from
> current program unit
> In file _egb.f:687
>
> charge(qmmm_nml%iqmatoms(qm_temp_count)) = &
> 1
> Error: Unclassifiable statement at (1)
> In file _egb.f:701
>
> charge(qmmm_nml%iqmatoms(qm_temp_count)) = &
> 1
> Error: Unclassifiable statement at (1)
> In file _egb.f:781
>
> maxi = natom
> 1
> Error: Name 'natom' at (1) is an ambiguous reference to 'natom' from
> current program unit
> In file _egb.f:782
>
> if(natbel > 0) maxi = natbel
> 1
> Error: Name 'natbel' at (1) is an ambiguous reference to 'natbel' from
> current program unit
> In file _egb.f:804
>
> sumdeijda(1:natom) = zero
> 1
> Error: Name 'natom' at (1) is an ambiguous reference to 'natom' from
> current program unit
> In file _egb.f:830
>
> iaci = ntypes * (iac(i) - 1)
> 1
> Error: Name 'ntypes' at (1) is an ambiguous reference to 'ntypes' from
> current program unit
> In file _egb.f:846
>
> do k=i+1,natom
> 1
> Error: Name 'natom' at (1) is an ambiguous reference to 'natom' from
> current program unit
> ..
>
> ....
> ....
> ....
>
> Thanks again for your help!
>
> Xin
>
> On Mon, 14 May 2012 19:22:58 -0700, Jason Swails
<jason.swails.gmail.com>
> wrote:
>> Did you do the "make depend" step I mentioned?
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>>
>> On May 14, 2012, at 6:01 PM, Xin Geng <xingeng2011.berkeley.edu> wrote:
>>
>>> On Mon, 14 May 2012 17:10:10 -0700, Jason Swails
> <jason.swails.gmail.com>
>>> wrote:
>>>> On Mon, May 14, 2012 at 3:55 PM, Xin Geng <xingeng2011.berkeley.edu>
>>> wrote:
>>>>
>>>>>
>>>>>
>>>>> Dear all,
>>>>>
>>>>> I want to implement a solvation energy function
>>>>> HPMF(Hydrophobic Potential of Mean Force[1])in Amber in order to use
>>>>> calculate thermodynamics integration of Amber+GB+HPMF. I wrote a
>>> program
>>>>> to
>>>>> implement HPMF. I enclosed my program to this email.
>>>>>
>>>>> However I have
>>>>> trouble in compiling my program with the Amber package. So, I want
to
>>> ask
>>>>> what modification I should to do with Amber Package to call the
>>>>> subroutines
>>>>> of my program.
>>>>>
>>>>
>>>>> From what I can tell, you wrote a module. A couple comments.
> Include
>>> the
>>>> dprec.h header (you seem to have done this already, but look at other
>>>> source files to see how this header is included -- i.e. #include
>>>> "../include/dprec.fh")
>>>>
>>>> This header defines a macro _REAL_ which you should use to define all
>>>> floating point data types (don't use real). This really only works
> with
>>>> double precision at this point. I think this is safer than using
> "real"
>>>> and "real*8" like you do...
>>>>
>>>> Afterwards, make sure your source code file is in
> $AMBERHOME/src/sander,
>>>> then run the command "make depend" in order to update the
> dependencies.
>>>>
>>>> Other than these comments, I think you would need to provide details
>>> about
>>>> exactly what you did and what error messages you got.
>>>>
>>>> HTH,
>>>> Jason
>>>>
>>>> P.S. -- you should also tell us what version of Amber you are trying
> to
>>> add
>>>> this to, since the exact instructions depend on that version.
>>>
>>> Hi Jason,
>>>
>>> Thanks for your help!
>>>
>>> I copy my file into $AMBERHOME/src/sander and include some header by
>>> referring icosasurf.f, such as assert.h, dprec.h and memory.h.
>>> I try to add this file to Amber10.
>>> I'll show you what I've done as follows:
>>> (1) Add "use genhpmf, only : init_hpmf" into subroutine force (Line 22
> of
>>> force.f) and "call init_hpmf(x,ix,ih,natom,nbona)" into subroutine
>>> force(Line 921 of force.f)
>>> (2) Add " use genhpmf !for HPMF calculation" into subroutine egb(Line
> 172
>>> of egb.f) and "if" from line 1614 of egb.f
>>>
>>> if (gbsa == 3) then
>>>
>>> !-----calculate hpmf instead of sasa
>>> !return value is esurf, teh file is ehpmf.f
>>>
>>> totsasa = 0
>>> esurf = ehpmf()
>>> end if !(gbsa == 3)
>>>
>>> When I use "make serial", the following errors show up:
>>>
>>> gfortran -c -O3 -fno-range-check -fno-second-underscore -ffree-form
-o
>>> egb.o _egb.f
>>> In file _egb.f:243
>>>
>>> use genhpmf !for HPMF calculation
>>> 1
>>> Fatal Error: Can't open module file 'genhpmf.mod' for reading at (1):
> No
>>> such file or directory
>>> make[1]: *** [egb.o] Error 1
>>> make[1]: Leaving directory `/home1/xingeng/HPMF/Amber10/src/sander'
>>> make: *** [serial] Error 2
>>>
>>> Thanks,
>>>
>>> Xin
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu May 17 2012 - 17:00:03 PDT
