diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 8c2ddfa5a0..c6c11ba095 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -58,8 +58,7 @@ Examples be changed without reparameterizing the entire model. They are provided in forms compatible with both *units lj* and *units real* (see documentation of :doc:`units `). These can also be read from a potential file with correct unit style by specifying the name - of the file. Several potential files for each unit style are included in the - /potentials/ directory of the LAMMPS distribution. + of the file. Several potential files for each unit style are included in the /potentials/ directory of the LAMMPS distribution. Description """"""""""" @@ -146,7 +145,7 @@ For each style oxdna, oxdna2 and oxrna2, the first parameter argument can be a f bond_style oxdna/fene bond_coeff * oxdna.lj -will be interpreted as a request to read the (FENE) potential :ref:`(Ouldridge) ` parameters from the file with the given name. +will be interpreted as a request to read the (FENE) potential :ref:`(Ouldridge) ` parameters from the file with the given name. The file can define multiple potential parameters for both bonded and pair interactions, but for the above bonded interactions there must exist in the file a line of the form: .. code-block:: LAMMPS @@ -154,8 +153,7 @@ The file can define multiple potential parameters for both bonded and pair inter * fene epsilon delta r0 There are sample potential files for each unit style in the /potentials/ directory of the LAMMPS distribution. The potential file unit system must align with -the units defined via the :doc:`units ` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ -directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/. +the units defined via the :doc:`units ` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/. ---------- diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index 4a0ef0d168..f5dc0fd94e 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -90,8 +90,7 @@ Examples .. note:: The coefficients in the above examples are provided in forms compatible with both *units lj* and *units real* (see documentation of :doc:`units `). - These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the - /potentials/ directory of the LAMMPS distribution. + These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the /potentials/ directory of the LAMMPS distribution. Description """"""""""" @@ -159,8 +158,7 @@ For each pair style above the first non-modifiable argument can be a filename, a pair_coeff 1 4 oxdna/hbond seqav oxdna.lj -will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name. -The file can define multiple potential parameters for both bonded and pair interactions, but for the example pair interaction above there must exist in the file a line of the form: +will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name. The file can define multiple potential parameters for both bonded and pair interactions, but for the example pair interaction above there must exist in the file a line of the form: .. code-block:: LAMMPS @@ -182,8 +180,7 @@ If potential customization is required, the potential file reading can be mixed will read the stacking and coaxial stacking potential parameters from the manual specification and all others from the potential file *oxdna.lj*. There are sample potential files for each unit style in the /potentials/ directory of the LAMMPS distribution. The potential file unit system must align with -the units defined via the :doc:`units ` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ -directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/. +the units defined via the :doc:`units ` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/. ---------- diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 38778edc09..1c7bd2ae8f 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -102,8 +102,7 @@ Examples .. note:: The coefficients in the above examples are provided in forms compatible with both *units lj* and *units real* (see documentation of :doc:`units `). - These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the - /potentials/ directory of the LAMMPS distribution. + These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the /potentials/ directory of the LAMMPS distribution. Description """"""""""" @@ -170,7 +169,7 @@ Therefore the following command: pair_coeff 1 4 oxdna2/hbond seqdep oxdna.real -will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name. +will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name. The file can define multiple potential parameters for both bonded and pair interactions, but for the example pair interaction above there must exist in the file a line of the form: .. code-block:: LAMMPS @@ -194,8 +193,7 @@ If potential customization is required, the potential file reading can be mixed will read the excluded volume and Debye-Hueckel effective charge *qeff* parameters from the manual specification and all others from the potential file *oxdna2.lj*. There are sample potential files for each unit style in the /potentials/ directory of the LAMMPS distribution. The potential file unit system must align with -the units defined via the :doc:`units ` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ -directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/. +the units defined via the :doc:`units ` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/. ---------- diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 0ea55c889e..60bbbd6fef 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -41,7 +41,7 @@ Syntax *oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) - T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K) + T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K) xi = 1.40206 (LJ units) or 8.35864576375849 (real units), temperature-independent coefficient in stacking strength kappa = 2.77 (LJ units) or 0.005504556 (real units), coefficient of linear temperature dependence in stacking strength *oxrna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -106,8 +106,7 @@ Examples .. note:: The coefficients in the above examples are provided in forms compatible with both *units lj* and *units real* (see documentation of :doc:`units `). - These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the - /potentials/ directory of the LAMMPS distribution. + These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the /potentials/ directory of the LAMMPS distribution. Description """"""""""" @@ -174,7 +173,7 @@ Therefore the following command: pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj -will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name. +will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name. The file can define multiple potential parameters for both bonded and pair interactions, but for the example pair interaction above there must exist in the file a line of the form: .. code-block:: LAMMPS @@ -199,8 +198,7 @@ If potential customization is required, the potential file reading can be mixed will read the excluded volume and Debye-Hueckel effective charge *qeff* parameters from the manual specification and all others from the potential file *oxrna2.lj*. There are sample potential files for each unit style in the /potentials/ directory of the LAMMPS distribution. The potential file unit system must align with -the units defined via the :doc:`units ` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ -directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/. +the units defined via the :doc:`units ` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/. ---------- diff --git a/src/CG-DNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp index 7a60ae3555..623963e925 100644 --- a/src/CG-DNA/bond_oxdna_fene.cpp +++ b/src/CG-DNA/bond_oxdna_fene.cpp @@ -225,7 +225,7 @@ void BondOxdnaFene::compute(int eflag, int vflag) ebond = -0.5 * k[type] * log(rlogarg); } - // switching to capped force for r-r0 -> Delta at + // switching to capped force for r-r0 -> Delta at // r > r_max = r0 + Delta*sqrt(1-rlogarg) OR // r < r_min = r0 - Delta*sqrt(1-rlogarg) if (rlogarg < rlogarg_min) { @@ -356,7 +356,7 @@ void BondOxdnaFene::coeff(int narg, char **arg) } if (iloc != arg[0] || potential_name != "fene") error->one(FLERR, "No corresponding fene potential found in file {} for bond type {}", arg[1], arg[0]); } - + MPI_Bcast(&k_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&Delta_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&r0_one, 1, MPI_DOUBLE, 0, world); diff --git a/src/CG-DNA/constants_oxdna.cpp b/src/CG-DNA/constants_oxdna.cpp index f3623f4dab..0c5ff27149 100644 --- a/src/CG-DNA/constants_oxdna.cpp +++ b/src/CG-DNA/constants_oxdna.cpp @@ -60,9 +60,9 @@ void ConstantsOxdna::set_real_units() // oxRNA 2 parameters in real units // d_cs_x = -3.4072 = d_cs for RNA d_cs_z = +1.7036; - d_cst_x_3p = +3.4072, + d_cst_x_3p = +3.4072; d_cst_y_3p = +0.8518; - d_cst_x_5p = +1.063949977, + d_cst_x_5p = +1.063949977; d_cst_y_5p = -0.07378929747; }; diff --git a/src/CG-DNA/pair_oxdna2_dh.cpp b/src/CG-DNA/pair_oxdna2_dh.cpp index 7f38c4b96f..582a635567 100644 --- a/src/CG-DNA/pair_oxdna2_dh.cpp +++ b/src/CG-DNA/pair_oxdna2_dh.cpp @@ -306,7 +306,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg) T = utils::numeric(FLERR,arg[2],false,lmp); rhos_dh_one = utils::numeric(FLERR,arg[3],false,lmp); - + if (utils::strmatch(arg[4], "^[a-zA-Z0-9]*\\.[a-zA-Z]+$") == true) { // if last arg is a potential file if (comm->me == 0) { // read value from potential file PotentialFileReader reader(lmp, arg[4], "oxdna potential", " (dh)"); diff --git a/src/CG-DNA/pair_oxdna_excv.cpp b/src/CG-DNA/pair_oxdna_excv.cpp index 3a98712818..0b8452a12b 100644 --- a/src/CG-DNA/pair_oxdna_excv.cpp +++ b/src/CG-DNA/pair_oxdna_excv.cpp @@ -574,7 +574,7 @@ void PairOxdnaExcv::coeff(int narg, char **arg) } if (iloc != arg[0] || jloc != arg[1] || potential_name != "excv") error->one(FLERR, "No corresponding excv potential found in file {} for pair type {} {}", arg[2], arg[0], arg[1]); } - + MPI_Bcast(&epsilon_ss_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&sigma_ss_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&cut_ss_ast_one, 1, MPI_DOUBLE, 0, world); @@ -587,7 +587,7 @@ void PairOxdnaExcv::coeff(int narg, char **arg) MPI_Bcast(&sigma_bb_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&cut_bb_ast_one, 1, MPI_DOUBLE, 0, world); } - + // smoothing - determined through continuity and differentiability b_ss_one = 4.0/sigma_ss_one *(6.0*pow(sigma_ss_one/cut_ss_ast_one,7)-12.0*pow(sigma_ss_one/cut_ss_ast_one,13)) diff --git a/src/CG-DNA/pair_oxdna_hbond.cpp b/src/CG-DNA/pair_oxdna_hbond.cpp index 4763f7412d..ba9d3ca610 100644 --- a/src/CG-DNA/pair_oxdna_hbond.cpp +++ b/src/CG-DNA/pair_oxdna_hbond.cpp @@ -776,7 +776,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) MPI_Bcast(&a_hb3_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&theta_hb3_0_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&dtheta_hb3_ast_one, 1, MPI_DOUBLE, 0, world); - + MPI_Bcast(&a_hb4_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&theta_hb4_0_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&dtheta_hb4_ast_one, 1, MPI_DOUBLE, 0, world); diff --git a/src/CG-DNA/pair_oxdna_stk.cpp b/src/CG-DNA/pair_oxdna_stk.cpp index 7991288c1e..ca9ad7a45b 100644 --- a/src/CG-DNA/pair_oxdna_stk.cpp +++ b/src/CG-DNA/pair_oxdna_stk.cpp @@ -868,7 +868,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) cosphi_st1_ast_one = values.next_double(); a_st2_one = values.next_double(); cosphi_st2_ast_one = values.next_double(); - + break; } else continue; } catch (std::exception &e) { diff --git a/src/CG-DNA/pair_oxdna_xstk.cpp b/src/CG-DNA/pair_oxdna_xstk.cpp index af80046b50..5bc0bbb874 100644 --- a/src/CG-DNA/pair_oxdna_xstk.cpp +++ b/src/CG-DNA/pair_oxdna_xstk.cpp @@ -751,7 +751,7 @@ void PairOxdnaXstk::coeff(int narg, char **arg) MPI_Bcast(&cut_xst_c_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&cut_xst_lo_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&cut_xst_hi_one, 1, MPI_DOUBLE, 0, world); - + MPI_Bcast(&a_xst1_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&theta_xst1_0_one, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&dtheta_xst1_ast_one, 1, MPI_DOUBLE, 0, world); diff --git a/src/CG-DNA/pair_oxrna2_xstk.cpp b/src/CG-DNA/pair_oxrna2_xstk.cpp index c5f4218d8f..ff70740589 100644 --- a/src/CG-DNA/pair_oxrna2_xstk.cpp +++ b/src/CG-DNA/pair_oxrna2_xstk.cpp @@ -675,7 +675,7 @@ void PairOxrna2Xstk::coeff(int narg, char **arg) a_xst8_one = values.next_double(); theta_xst8_0_one = values.next_double(); dtheta_xst8_ast_one = values.next_double(); - + break; } else continue; } catch (std::exception &e) {