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Messages - Yu_Zhuochen

#1
I've run these following commands,and try to install raspa3 on ubuntu:
$sudo apt install build-essential git cmake
$sudo add-apt-repository 'deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy-18 main'
$sudo add-apt-repository 'deb-src http://apt.llvm.org/jammy/ llvm-toolchain-jammy-18 main'
$sudo apt install libllvm-18-ocaml-dev libllvm18 llvm-18 llvm-18-dev llvm-18-runtime
$sudo apt install libc++-18-dev libc++abi-18-dev libomp-18-dev pybind11-dev python3-pybind11 liblapack-dev clang-tools-18
$cd src
$vi makefile-manual  and set CXX=clang++-18
$make -f makefile-manual
However, there are several errors during installation:

In module 'std_atomic' imported from foundationkit/threadpool.ixx:31:
In module 'std_private_atomic_aliases' imported from /usr/lib/llvm-18/bin/../include/c++/v1/atomic:591:
In module 'std_cstdlib' imported from /usr/lib/llvm-18/bin/../include/c++/v1/__atomic/aliases.h:21:
/usr/lib/llvm-18/bin/../include/c++/v1/stdlib.h:123:59: error: 'abs' has different definitions in different modules; definition in module 'std_cstdlib' first difference is function body
  123 | _LIBCPP_NODISCARD_EXT inline _LIBCPP_HIDE_FROM_ABI double abs(double __lcpp_x) _NOEXCEPT {
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  124 |   return __builtin_fabs(__lcpp_x);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 | }
      | ~
/usr/lib/llvm-18/bin/../include/c++/v1/stdlib.h:123:59: note: but in '' found a different body
  123 | _LIBCPP_NODISCARD_EXT inline _LIBCPP_HIDE_FROM_ABI double abs(double __lcpp_x) _NOEXCEPT {
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  124 |   return __builtin_fabs(__lcpp_x);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 | }
      | ~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [makefile-manual:47: foundationkit/threadpool.pcm] Error 1

How can I solve this problem?
#2
Could you please show the input file?
#3
Simulation algorithms and theory / Re: MSD of MD
February 24, 2023, 01:47:10 PM
I met the same problem. How to solve it?
#4
Dear Prof. Dubbeldam:
I am trying to use GenericMOFs forcefield to make simulations of CO2/H2 adsorption among a database containing 600 COFs. Previouse researchers have already reported some results about 10 COFs with the best performance from the CORE-COF-2020 database(CO2/H2 separation, 0.15:0.85, 1bar-298K&0.1bar-298K).
When I try to reproduce simulation from a previous paper(J. Phys. Chem. C 2020, 124, 22577−22590), even if I set all parameters totally the same as the paper did(forcefiled:DREIDING(I choose GenericMOFs in RASPA), CutOFFVDW 14.0, CO2&H2 are found from share/molecues/TraPPE).
I choosed 5 COFs structures: NPN-2, COF-42-gra, FLT-COF-1, COF-JLU3, PyTTA-BFBIm-iCOF as a test case.

However, my simulation results don't match the paper at all!
I found that some cifs have such a form:
data_TpMA
_audit_creation_date              2022-07-26
_audit_creation_method            'Materials Studio'
_symmetry_space_group_name_H-M    'P1'
_symmetry_Int_Tables_number       1
_symmetry_cell_setting            triclinic
loop_
_symmetry_equiv_pos_as_xyz
  x,y,z
_cell_length_a                    11.2024
_cell_length_b                    11.2061
_cell_length_c                    3.4772
_cell_angle_alpha                 97.1070
_cell_angle_beta                  91.6120
_cell_angle_gamma                 119.7344
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
xx1    C     0.47506   0.43704   0.52016   0.00000  Uiso   1.00
xx2    N     0.50682   0.55667   0.42256   0.00000  Uiso   1.00
xx3    O     0.77447   0.62245   0.71005   0.00000  Uiso   1.00
xx4    C     0.41472   0.61064   0.42851   0.00000  Uiso   1.00
xx5    N     0.27729   0.52657   0.44818   0.00000  Uiso   1.00
xx6    C     0.57467   0.38607   0.51378   0.00000  Uiso   1.00
xx7    C     0.71912   0.47896   0.59883   0.00000  Uiso   1.00
xx8    C     0.56333   0.03745   0.42485   0.00000  Uiso   1.00
xx9    N     0.43518   0.94910   0.46020   0.00000  Uiso   1.00
xx10   O     0.38447   0.14605   0.30057   0.00000  Uiso   1.00
xx11   C     0.38143   0.80299   0.44908   0.00000  Uiso   1.00
xx12   N     0.46618   0.74843   0.42631   0.00000  Uiso   1.00
xx13   C     0.61505   0.18930   0.46498   0.00000  Uiso   1.00
xx14   C     0.52400   0.24103   0.42915   0.00000  Uiso   1.00
xx15   C     0.96190   0.52887   0.59917   0.00000  Uiso   1.00
xx16   N     0.04773   0.48874   0.48793   0.00000  Uiso   1.00
xx17   O     0.84383   0.22694   0.60631   0.00000  Uiso   1.00
xx18   C     0.19208   0.58005   0.47129   0.00000  Uiso   1.00
xx19   N     0.24457   0.71864   0.47369   0.00000  Uiso   1.00
xx20   C     0.81129   0.42768   0.58297   0.00000  Uiso   1.00
xx21   C     0.75811   0.28227   0.54563   0.00000  Uiso   1.00
xx22   H     0.37400   0.37256   0.61288   0.00000  Uiso   1.00
xx23   H     0.71304   0.64860   0.86224   0.00000  Uiso   1.00
xx24   H     0.63606   0.00100   0.38331   0.00000  Uiso   1.00
xx25   H     0.33038   0.18685   0.19256   0.00000  Uiso   1.00
xx26   H     0.99955   0.63885   0.68662   0.00000  Uiso   1.00
xx27   H     0.92695   0.28844   0.80338   0.00000  Uiso   1.00

When RASPA load an atom named xx, it cannot be read.
How can I do to solve this problem?
#5
Input files and parameters / Re: pseudo_atom radii
February 09, 2023, 03:54:22 AM
Dear Prof. :
I wonder how to calculate the radii when we simulate a flexible molecue or framework indeed.

Sincerely.