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MEMD (SCAFACOS) interfacing issue


From: Keerthi Radhakrishnan 150503
Subject: MEMD (SCAFACOS) interfacing issue
Date: Sat, 25 Sep 2021 19:43:49 +0530

Dear all,

I am a PhD student currently pursuing research in soft matter physics. My work mostly deals with charged polymeric systems. Presently, my project at hand demands the incorporation of dielectric variation  within the solvent in the  presence of explicit charges. For that I resort to the MEMD solver included in SCAFACOS library for the electrostatics. This is the code snippet from my pypresso script where it incubates MEMD following  the instructions given in the espresso manual.

from espressomd.electrostatics import Scafacos
from espressomd.electrostatics import Scafacos
scafacos = Scafacos(prefactor=1, method_name="memd", method_params={"timestep": 0.005, "mesh": 1, "temperature":1, "bjerrum_length":3})
system.actors.add(scafacos)
 
Following this I get an  error regarding the unrecognition of the passed argument, which I have carefully taken the argument names mentioned in SCAFACOS manual itself for MEMD Solver-specific parameters. If this is not the case of how arguments are named, then where in espresso documentations is anything regarding it given.


The ERROR is follows:
New handle created!
terminate called after throwing an instance of 'std::runtime_error'
  what():  interface (parser): error in parameter string at 'timestep'!
[Langevin:04113] *** Process received signal ***
[Langevin:04113] Signal: Aborted (6)
[Langevin:04113] Signal code:  (-6)
[Langevin:04113] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3efd0)[0x7f58ac287fd0]
[Langevin:04113] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f58ac287f47]
[Langevin:04113] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f58ac2898b1]
[Langevin:04113] [ 3] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8c957)[0x7f58a9d42957]
[Langevin:04113] [ 4] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92ae6)[0x7f58a9d48ae6]
[Langevin:04113] [ 5] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92b21)[0x7f58a9d48b21]
[Langevin:04113] [ 6] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92d54)[0x7f58a9d48d54]
[Langevin:04113] [ 7] /home/system1/espresso/test_build2/src/scafacos/Scafacos.so(_ZN8Scafacos8Scafacos16parse_parametersERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x68)[0x7f58a1931938]
[Langevin:04113] [ 8] /home/system1/espresso/test_build2/src/scafacos/Scafacos.so(_ZN8Scafacos8ScafacosC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEP19ompi_communicator_tS8_+0xca)[0x7f58a1931a1a]
[Langevin:04113] [ 9] /home/system1/espresso/test_build2/src/core/EspressoCore.so(+0x25261d)[0x7f58aa79d61d]
[Langevin:04113] [10] /home/system1/espresso/test_build2/src/core/EspressoCore.so(_ZN8Scafacos14set_parametersERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_b+0x3a6)[0x7f58aa79dab6]
[Langevin:04113] [11] /home/system1/espresso/test_build2/src/python/espressomd/scafacos.so(+0xb651)[0x7f58084c3651]
[Langevin:04113] [12] /home/system1/espresso/test_build2/src/python/espressomd/electrostatics.so(+0x39c3d)[0x7f5808704c3d]
[Langevin:04113] [13] /home/system1/espresso/test_build2/src/python/espressomd/electrostatics.so(+0x39e0d)[0x7f5808704e0d]
[Langevin:04113] [14] /home/system1/espresso/test_build2/src/python/espressomd/electrostatics.so(+0x4ff46)[0x7f580871af46]
[Langevin:04113] [15] /home/system1/espresso/test_build2/src/python/espressomd/actors.so(+0xd47d)[0x7f585c92947d]
[Langevin:04113] [16] /home/system1/espresso/test_build2/src/python/espressomd/actors.so(+0xd64d)[0x7f585c92964d]
[Langevin:04113] [17] /home/system1/espresso/test_build2/src/python/espressomd/actors.so(+0x19b06)[0x7f585c935b06]
[Langevin:04113] [18] /home/system1/espresso/test_build2/src/python/espressomd/script_interface.so(+0x135ec)[0x7f589df195ec]
[Langevin:04113] [19] /home/system1/espresso/test_build2/src/python/espressomd/actors.so(+0xd47d)[0x7f585c92947d]
[Langevin:04113] [20] /home/system1/espresso/test_build2/src/python/espressomd/actors.so(+0xd64d)[0x7f585c92964d]
[Langevin:04113] [21] /home/system1/espresso/test_build2/src/python/espressomd/actors.so(+0x1146a)[0x7f585c92d46a]
[Langevin:04113] [22] /usr/bin/python3(_PyObject_FastCallKeywords+0x19c)[0x5a9d2c]
[Langevin:04113] [23] /usr/bin/python3[0x50a533]
[Langevin:04113] [24] /usr/bin/python3(_PyEval_EvalFrameDefault+0x444)[0x50bf44]
[Langevin:04113] [25] /usr/bin/python3[0x507cd4]
[Langevin:04113] [26] /usr/bin/python3(PyEval_EvalCode+0x23)[0x50ae13]
[Langevin:04113] [27] /usr/bin/python3[0x635262]
[Langevin:04113] [28] /usr/bin/python3(PyRun_FileExFlags+0x97)[0x635317]
[Langevin:04113] [29] /usr/bin/python3(PyRun_SimpleFileExFlags+0x17f)[0x638acf]
[Langevin:04113] *** End of error message ***
Aborted (core dumped)


Following, this I also figured that the interface file in scafacos:    scafacos-fcs-0.1/src/FCSInterface.c  - line 1633 the part where arguments for memd is defined is commented. Don't know if this has anything to do with the existing issue. 
An insight into the root of this problem and a practical resolve to it would be highly appreciated.
 
Regards
Keerthi 

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