Hello,
I found another problems in actual paramfit version (including AT patch 7).
These are related to the SCATTERPLOTS option which in actual version
works fully just for dihedrals.
Below are listed all problematic lines (the first one in given pair) and
corrected versions (the second one in given pair). After all these
corrections
SCATTERPLOTS option works as it should (i.e. as it is declared in the
manual).
in FILE bounds_check.c
line 382
if (parm_data->angle_data[param].DO_FIT_THEQ==YES)
if (parm_data->angle_data[param].DO_FIT_THEQ==YES ||
parm_data->angle_data[param].DO_FIT_KT==YES)
line 511
if (parm_data->bond_data[param].DO_FIT_REQ==YES)
if (parm_data->bond_data[param].DO_FIT_REQ==YES ||
parm_data->bond_data[param].DO_FIT_KR==YES)
line 516
sprintf(filename, "%d.bondeq\n", param);
sprintf(filename, "%d.bondeq", param);
line 518
fprintf(plot, filename, "%s-%s", parm_data->bond_data[param].atom_type1,
parm_data->bond_data[param].atom_type2);
fprintf(plot, "#%s-%s\n", parm_data->bond_data[param].atom_type1,
parm_data->bond_data[param].atom_type2);
line 520
fprintf(plot, "%f\n", bounds_data->bond_lengths[param][pos]);
fprintf(plot, "%f 1\n", bounds_data->bond_lengths[param][pos]);
Best wishes,
Marek
Dne Tue, 29 Jul 2014 03:25:16 +0200 Marek Maly <marek.maly.ujep.cz>
napsal/-a:
> Hi Robin,
>
> indeed that I used the the actual paramfit including patch7
> to create the parameters.in and so the problem which I discussed
> is related to the latest format of this file having these strings:
>
> #### BOND REQ KR ####
> #### ANGLE KT THEQ ####
> #### DIHEDRAL TERM KP NP PHASE ####
>
> as the "signals" to start interpret next line as the useful data
> and where # alone is the "STOP" signal (in case of BOND and ANGLE
> section).
>
>
> Best wishes,
>
> Marek
>
>
> Dne Tue, 29 Jul 2014 02:52:14 +0200 Robin Betz <rbetz.ucsd.edu>
> napsal/-a:
>
>> Hi Marek,
>>
>> As stated in the update.7 bugfix info, there have been some improvements
>> to
>> the parameters to fit file format that result in old files being
>> incompatible. Re-generate this file using the SET_PARAMS runtype and it
>> should work again. Rest assured all versions of paramfit undergo
>> thorough
>> testing for all typical use cases.
>>
>> A tutorial on paramfit is being prepared and will be released very soon,
>> which will provide a full explanation of all job control options and
>> more
>> importantly a discussion of how to evaluate the resulting parameters for
>> quality.
>>
>> Hope this helps,
>> Robin
>>
>>
>> On Mon, Jul 28, 2014 at 1:51 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>>
>>> Hi Robin,
>>>
>>> thanks for the complex info. I have also one more for you :))
>>>
>>> After successful applying of the patch 7, the paramfit
>>> was not able to read angle parameters from the file where
>>> all the parameters for fitting was previously saved (i.e.
>>> parameters.in).
>>>
>>> SOLUTION:
>>>
>>> In "file_io.c" in function "read_parameter_file_v2" (cca lines 201-206)
>>>
>>> change:
>>>
>>> }
>>> } while (strncmp(line, "#### ANGL", 9)!=0);
>>>
>>> // Read in the angles
>>> while (strncmp(line,"#",1)!=0) {
>>> fgets(line,127,fptr);
>>>
>>> TO
>>>
>>> }
>>> } while (strncmp(line, "#### ANGL", 9)!=0);
>>>
>>> // Read in the angles
>>> fgets(line,127,fptr);
>>> while (strncmp(line,"#",1)!=0) {
>>>
>>> i.e. the first fgets in the "// Read in the angles" while cycle
>>> has to be placed before while header (the same as in bond section)
>>> otherwise,
>>> the "// Read in the angles" cycle will be skipped because in "line"
>>> variable
>>> is "#### ANGLE KT THEQ ####" at the moment when the
>>> "strncmp(line,"#",1)!=0" condition is firstly checked in the "// Read
>>> in
>>> the angles" cycle and so this condition has on the very
>>> start of the angle part value FALSE.
>>>
>>> Anyway would be a good idea to test functionality of any updated part
>>> of
>>> the software before
>>> it is released :))
>>>
>>> Regarding SEARCH_SPACE I checked the genetic algorithm part and I
>>> started
>>> to have doubts
>>> that the given implementation could guarantee the final results within
>>> the
>>> SEARCH_SPACE relative range around the initial value. So thanks for the
>>> confirmation.
>>> Anyway something like your actual explanation should be placed in the
>>> Amber14 manual because
>>> the actual comments related to SEARCH_SPACE clearly suggest in my
>>> opinion,
>>> that the final
>>> values should be in SEARCH_SPACE relative distance from the initial
>>> values
>>> independently
>>> from the quality of the initial guesses.
>>>
>>> Thanks again,
>>>
>>> Best wishes,
>>>
>>> Marek
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Dne Mon, 28 Jul 2014 22:12:58 +0200 Robin Betz <rbetz.ucsd.edu>
>>> napsal/-a:
>>>
>>>
>>> Hi Marek,
>>>>
>>>> Thanks for your helpful bug report. I appreciate the time you took to
>>>> look
>>>> at the code to figure out the source of each error. I've addressed
>>>> each of
>>>> your bugs as follows:
>>>>
>>>> 1. Fixed in update.7.
>>>>
>>>> 2. Fixed in the development tree. A workaround is just to pass the -c
>>>> and
>>>> -p parameters in the case of only one input topology.
>>>>
>>>> 3. There were two bugs causing the issue you saw. Both are now fixed
>>>> in
>>>> the
>>>> development tree.
>>>>
>>>> First, if a job control file is passed to paramfit without any
>>>> topology
>>>> files (the -i option only), the program will segfault for the reasons
>>>> you
>>>> identified. This set of inputs doesn't make sense though, as if a job
>>>> control file is inputted there is no need for the wizard, but there is
>>>> no
>>>> topology file to act upon. In this case paramfit will now output an
>>>> error
>>>> about inconsistent command line options.
>>>>
>>>> Secondly, if a job control file and a parameter file are passed to
>>>> paramfit
>>>> (the -i and -p/-pf options), and the NSTRUCTURES=<number> line is
>>>> present
>>>> in the job control file, the program will segfault. This is because
>>>> the
>>>> number of structures is a property of the coordinate structure, which
>>>> has
>>>> not been allocated due to the absence of the -c/-cf command line
>>>> options.
>>>> Paramfit will now output an error if this scenario is present. This is
>>>> also
>>>> why it might have worked with your input files but not with the wizard
>>>> ones, as the NSTRUCTURES line is always present in the files that the
>>>> wizard writes.
>>>>
>>>> A workaround for this is to always pass a topology and coordinate file
>>>> to
>>>> paramfit.
>>>>
>>>> 4. This is normal behavior. To clarify, the SEARCH_SPACE parameter
>>>> only
>>>> affects the starting population of the genetic algorithm, and the
>>>> final
>>>> parameters are free to be outside this range. The parameters in the
>>>> population can drift from the starting range by either the mutation
>>>> operation or the simplex refinement. If you're repeatedly seeing
>>>> convergence to other values there is most likely a very large
>>>> difference
>>>> in
>>>> fitness between your starting search area and where the algorithm ends
>>>> up.
>>>> You can encourage the algorithm to remain in certain areas of
>>>> parameter
>>>> space by reducing the mutation rate (MUTATION_RATE=<0-1.0>) and
>>>> removing
>>>> the simplex refinements altogether (GENERATIONS_TO_SIMPLEX=0).
>>>>
>>>> I will let you know when the next official patch is released.
>>>> Thanks again,
>>>>
>>>> Robin
>>>>
>>>>
>>>> On Sun, Jul 27, 2014 at 9:12 AM, Marek Maly <marek.maly.ujep.cz>
>>>> wrote:
>>>>
>>>> Hi Robin and all,
>>>>>
>>>>> I analyzed some of the actual paramfit problems (the most of all
>>>>> I mentioned before except the SEARCH_SPACE parameter problem).
>>>>> I am also suggesting some solutions for those who would like
>>>>> to use it before the proper patch will be released.
>>>>>
>>>>> Solved/analyzed problems:
>>>>>
>>>>> #1
>>>>> Ignoration of the K value if this should be read in from the "Job
>>>>> Control
>>>>> File" (JCF)
>>>>> or from the prmtop_list file.
>>>>>
>>>>> SOLUTION:
>>>>>
>>>>> in file "process_prmtop.c" , in line : 397 (func.
>>>>> process_single_prmtop)
>>>>> comment (//) or delete "parm_data->K=0.".
>>>>> There is too late for default setting of this parameter at this
>>>>> place.
>>>>>
>>>>> #2
>>>>> Paramfit crashes when one uses prmtop_list and mdcrd_list approach
>>>>> (i.e. paramfit -i Job_Control.in -pf prmtop_list -cf mdcrd_list -v
>>>>> MEDIUM
>>>>> --random-seed seed )
>>>>> in the case that there is just one prmtop/mdcrd file (just one
>>>>> molecule).
>>>>>
>>>>> This should not happen even if in such a case one may use recommended
>>>>> way
>>>>> for one molecule fit,
>>>>> without using prmtop_list and mdcrd_list.
>>>>> (i.e. paramfit -i Job_Control.in -p prmtop -c mdcrd -q QM_data.dat )
>>>>>
>>>>> SOLUTION:
>>>>>
>>>>> in file "read_mdcrd.c", in line : 35 (func. read_mdcrds)
>>>>> change "if (global_options->num_prmtops>1)" to "if
>>>>> (global_options->num_prmtops>=1)"
>>>>>
>>>>> #3
>>>>> Paramfit crashes when one strts it without any parameters i.e. in
>>>>> "wizard
>>>>> mode" in
>>>>> the moment when K value is read in.
>>>>>
>>>>> REASON
>>>>>
>>>>> That critical moment corresponds to the line : 181 (func.
>>>>> job_control_wizard) where
>>>>> is written command: "parm_datas[0].K=get_float();"
>>>>> Unfortunately the pointer "parm_datas" has at this moment value NULL
>>>>> or
>>>>> (nil) (depend on compiler)
>>>>> which probably means that at this moment this pointer still dos not
>>>>> represent any parm_struct structure (no proper memmory allocation
>>>>> was
>>>>> done
>>>>> yet using parm_datas pointer).
>>>>>
>>>>> In this context is strange to me that the same problem does not
>>>>> occure in
>>>>> case when JCF is already created by hand (not by wizard).
>>>>>
>>>>> I would assume that the command "parm_data[0].K=double_temp1;" (line
>>>>> :
>>>>> 366
>>>>> in process_job_control_setting.c) will also cause the program crash
>>>>> here
>>>>> because it seems, that the parm_datas is used for the allocation of
>>>>> the
>>>>> parm_struct structures array in function "read_prmtops" which is in
>>>>> the
>>>>> main function (in parameter_optimiser.c) called after the calls of
>>>>> "read_job_control_file" OR "job_control_wizard".
>>>>>
>>>>> #4
>>>>> Parameter SEARCH_SPACE does not seem to be fully functional (this
>>>>> problem
>>>>> I had also in the previous versions of paramfit). At least in the
>>>>> case of
>>>>> the force constants there is some problem, otherwise it should not be
>>>>> possible that I get for one my angle force constant the final value
>>>>> -5.2256 if the starting value was 58.2894 and the SEARCH_SPACE
>>>>> parameter
>>>>> was set to value 0.5.
>>>>>
>>>>> In such a case I would expected that the final value of this force
>>>>> constant will be in the range from
>>>>> 58.2894 - 0.5*58.2894 to 58.2894 + 0.5*58.2894. Clearly the actual
>>>>> final
>>>>> value -5.2256 does not belong to this interval. I verified that there
>>>>> is
>>>>> not a problem with reading SEARCH_SPACE parameter from the JCF as the
>>>>> right
>>>>> value is clearly written in the screen. Anyway I just to be sure
>>>>> rewrote
>>>>> this value in "defaults.c" but this did not helped so the problem is
>>>>> clearly in the implementation/usage of this parameter.
>>>>>
>>>>> This problem is actual for GENETIC but also for SIMPLEX calculation
>>>>> mode.
>>>>>
>>>>> All the above described problems are related to the actual version
>>>>> of
>>>>> Amber Tools which are
>>>>> patched up to the patch 6.
>>>>>
>>>>> Patch 7 from the 17 July, where also some paramfit problems were
>>>>> addressed
>>>>> was
>>>>> not applied because it was not possible. I describe this in the
>>>>> separate
>>>>> email.
>>>>> But anyway above described problems are probably not fixed in p.7 as
>>>>> Robin
>>>>> wrote (25 July) that they will be fixed in some next patch.
>>>>>
>>>>> Best wishes,
>>>>>
>>>>>
>>>>> Marek
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Dne Fri, 25 Jul 2014 17:33:37 +0200 Robin Betz <rbetz.ucsd.edu>
>>>>> napsal/-a:
>>>>>
>>>>> Hi Marek,
>>>>>
>>>>>>
>>>>>> This is a known bug with paramfit and will be fixed in the next few
>>>>>> days.
>>>>>> I
>>>>>> will let you know when the update is released.
>>>>>>
>>>>>> Regards,
>>>>>> Robin Betz
>>>>>> On Jul 24, 2014 3:05 PM, "Marek Maly" <marek.maly.ujep.cz> wrote:
>>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>>>
>>>>>>> I just wanted to do some "revision" ff parameters fitting using the
>>>>>>> paramfit from the
>>>>>>> actual Amber14. When I tried to use this actual paramfit version
>>>>>>> for
>>>>>>> FIT
>>>>>>> work,
>>>>>>> I realized that the value of the constant K clearly written in the
>>>>>>> control
>>>>>>> file
>>>>>>> (K=-196.792733) was not read in and instead default value of K
>>>>>>> (i.e.
>>>>>>> 0.0000) is
>>>>>>> used and written in the screen.
>>>>>>> So I decided to use recommended wizard to create control file
>>>>>>> (however
>>>>>>> in
>>>>>>> case of
>>>>>>> the older paramfit versions I never had problem with control file
>>>>>>> created
>>>>>>> by hand).
>>>>>>>
>>>>>>> Unfortunately the wizard failed exactly in the step where it had
>>>>>>> to
>>>>>>> read
>>>>>>> K constant value,
>>>>>>> please see below. I verified this behavior on two different HW
>>>>>>> platforms.
>>>>>>>
>>>>>>> So it seems that the actual paramfit version (at least the my
>>>>>>> OpenMP
>>>>>>> version) has some problems
>>>>>>> in reading of the floating point numbers (from the file and as
>>>>>>> well
>>>>>>> from
>>>>>>> the screen (wizard)).
>>>>>>>
>>>>>>> I tried here to change the number of cores (using OMP_NUM_THREADS)
>>>>>>> from 8
>>>>>>> to 1 (for the wizard work) but this did not helped. I would be very
>>>>>>> grateful for any useful suggestions which could help me to
>>>>>>> solve this problem.
>>>>>>>
>>>>>>> I am using Amber14 with the patches up to 3 (in case of AT up to
>>>>>>> 6).
>>>>>>> My OS is CentOS release 6.5 (2.6.32-431.el6.x86_64), I used gnu
>>>>>>> compilers
>>>>>>> to compile Amber14 ( gcc version 4.4.7 20120313 (Red Hat 4.4.7-4)
>>>>>>> (GCC)
>>>>>>> ).
>>>>>>> I did not recognize any other problems (e.g. durin MD simulation)
>>>>>>> and
>>>>>>> all
>>>>>>> the
>>>>>>> tests which are recommended part of the Amber14 installation
>>>>>>> proceeded
>>>>>>> successfully.
>>>>>>>
>>>>>>> Thank you in advance for the help,
>>>>>>>
>>>>>>> Best wishes,
>>>>>>>
>>>>>>> Marek
>>>>>>>
>>>>>>>
>>>>>>> ! Setting verbosity to medium.
>>>>>>>
>>>>>>>
>>>>>>> *****************************************************
>>>>>>> * AMBER Bond Angle and Dihedral Parameter
>>>>>>> Optimiser *
>>>>>>> *
>>>>>>> *
>>>>>>> *
>>>>>>> v3.0.0 *
>>>>>>> *
>>>>>>> *
>>>>>>> * Written
>>>>>>> by: *
>>>>>>> * Robin Betz
>>>>>>> (2011) *
>>>>>>> * Ross Walker
>>>>>>> (2004) *
>>>>>>> * The Walker Molecular Dynamics
>>>>>>> Lab *
>>>>>>> * University of California, San
>>>>>>> Diego *
>>>>>>> * La Jolla, California,
>>>>>>> 92092 *
>>>>>>> *
>>>>>>> USA *
>>>>>>> *****************************************************
>>>>>>>
>>>>>>>
>>>>>>> ************************************************************
>>>>>>> *************************
>>>>>>> Execution started at:
>>>>>>> | Thu Jul 24 23:31:16 2014
>>>>>>>
>>>>>>> |
>>>>>>> | Running OpenMP version of code using 1
>>>>>>> processors
>>>>>>>
>>>>>>> | Random seed = 1406237476
>>>>>>> PARAMFIT SETTINGS WIZARD
>>>>>>> ------------------------
>>>>>>>
>>>>>>> Enter a job control filename to save settings as, or hit enter
>>>>>>> > control.in
>>>>>>> Saving job control settings as "control.in"
>>>>>>>
>>>>>>> How many input structures do you have?
>>>>>>> 100
>>>>>>>
>>>>>>> Which format is your coordinate file in?
>>>>>>> 1) Trajectory (.mdcrd,.inpcrd)
>>>>>>> 2) Restart (.rst, .restart)
>>>>>>> 1
>>>>>>>
>>>>>>> What type of job do you want to run?
>>>>>>> 1) Create input files for quantum program
>>>>>>> 2) Set which parameters to fit
>>>>>>> 3) Conduct a fit
>>>>>>> 3
>>>>>>>
>>>>>>> Which parameters would you like to fit?
>>>>>>> 1) Defaults (see manual)
>>>>>>> 2) Load list from file
>>>>>>> 3) K only
>>>>>>> > 2
>>>>>>> Enter file name:
>>>>>>> > parameters.in
>>>>>>> Enter the initial value for K:
>>>>>>> > -196.792733
>>>>>>> Error: signal 11:
>>>>>>> /opt/amber14/bin/paramfit[0x4090d5]
>>>>>>> /lib64/libc.so.6(+0x329a0)[0x7f83cdff79a0]
>>>>>>> /opt/amber14/bin/paramfit[0x421bf9]
>>>>>>> /opt/amber14/bin/paramfit[0x40a561]
>>>>>>> /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f83cdfe3d1d]
>>>>>>> /opt/amber14/bin/paramfit[0x401739]
>>>>>>> [mara.node25 04_FIT]$
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>>>>>>> http://www.opera.com/mail/
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>>
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>>>>> http://www.opera.com/mail/
>>>>>
>>>>> _______________________________________________
>>>> AMBER mailing list
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> --
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>>> http://www.opera.com/mail/
>>>
>>
>>
>>
>> __________ Informace od ESET NOD32 Antivirus, verze databaze 10167
>> (20140728) __________
>>
>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>
>> http://www.eset.cz
>>
>
>
--
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Received on Wed Jul 30 2014 - 14:00:02 PDT
