Commit 2e5dad69 authored by milafternoon's avatar milafternoon
Browse files

extra info in docs

parent ced0e590

docs/source/input_mods.rst

+2 −0
Original line number Diff line number Diff line
@@ -91,3 +91,5 @@ Modify nbfix :math:`\sigma`/:math:`\varepsilon` 


    nm HGA2 OG311



Note that 'n' refers to NBFIX-:math:`\sigma` and 'm' refers to NBFIX-:math:`\varepsilon`;

other cases should be intuitive ('c' for charge, 's' for sigma etc.)
 
 No newline at end of file

processing.py

+13 −13
Original line number Diff line number Diff line
@@ -67,7 +67,7 @@ def run_gromacs(args): 
    struct = structs_list[traj.top_num]

    tpr = top_core_name + '-rerun.tpr'

    if tpr not in os.listdir(folder_name):

        subprocess.call('{gmx} grompp -f {mdp} -p {top} -c {struct} -maxwarn 10 '

        subprocess.call('{gmx} grompp -f {mdp} -p {top} -c {struct} -maxwarn 50 '

                        '-o {fname}/{tpr} >> rerun.log 2>&1'.format(mdp=dyn_mdp, top=top_path, gmx=gmx, struct=struct,

                                                                    fname=folder_name, tpr=tpr), shell=True)

    if not alch:
@@ -89,7 +89,8 @@ def run_gromacs(args): 
                            '-o {fname}/{tn}-energy >> rerun.log 2>&1'.format(gmx=gmx, fname=folder_name, tn=traj_alias,

                                                                              en=energy, pcode=pot_code), shell=True)

        else:

            print("in mod {fname} skipping trajectory {tn}, already calculated".format(fname=folder_name, tn=traj_alias))

            print("in mod {fname} skipping trajectory {tn}, already calculated".format(fname=folder_name,

                                                                                       tn=traj_alias))

    else:

        if '{tn}-dhdl.xvg'.format(tn=traj_alias) not in os.listdir(folder_name):

            if tpr not in os.listdir(folder_name):
@@ -213,6 +214,7 @@ def parse_input_line(line, top, td): 
    subclass instances corresponding to the desired configuration.

    :param line: str, line from input

    :param top: a Top object that will be passed to create the instance

    :param td: the main ThermoDiff object

    :return: a list of Mod subclass instances

    """

    line_list = line.split()
@@ -222,6 +224,7 @@ def parse_input_line(line, top, td): 
    # case 1: dealing with charge/sigma/epsilon

    if all(x in 'cse' for x in mods):

        for mod in mods:

            ll = None

            if c == 0:

                ll = top.find_type(line_list[1])

            if c == 2:
@@ -255,8 +258,8 @@ def parse_input_line(line, top, td): 
                    else top[0].list_sections('angles')

                for s in sections:

                    molname = [x for x in top[0].mols.keys() if s in top[0].mols[x]][0]

                    for l in range(len(top[0].sections[s])):

                        lspl = top[0].sections[s][l].split()

                    for lnum in range(len(top[0].sections[s])):

                        lspl = top[0].sections[s][lnum].split()

                        if len(lspl) > (pars-1) and lspl[0][0] not in '[;' \

                                and check_line([top[0].nums_to_types[molname][lspl[i]] for i in range(pars)], ll):

                            n.append(tuple(top[0].nums_to_names[molname][lspl[i]].split('-')[2] for i in range(pars)))
@@ -345,6 +348,7 @@ def process_target_line(line, abs_path, trajset_dict, td): 
    :param line: str, line to process

    :param abs_path: str, absolute path to target.dat

    :param trajset_dict: dict, binds trajectory indices to trajectory group names

    :param td: the main ThermoDiff object

    :return: a Target instance

    """

    lspl = line.strip().split()
@@ -399,6 +403,7 @@ def process_targets(input_file, trajs_input, td): 
    target refinement

    :param input_file: str, input file for targets

    :param trajs_input: str, input file for trajectories

    :param td: the main ThermoDiff object

    :return: list, contains tuples of directives

    """

    trajs, trajsets = read_traj_params(trajs_input)
@@ -485,16 +490,11 @@ def check_line(list_line_to_check, list_entries): 




def plot_results(mods, q_num, axis):

    #q = mods[-1].qs[q_num]

    for m in range(len(mods)):

        axis.bar(x=m, height=mods[m].qs[q_num].target_improvement_per_unit_change, label=str(m))

    axis.legend()

    #  TODO draw profile

    #  TODO draw histogram

        # if q.profile:

        #     axis.plot(q.diff, label=str(m))

        # else:

        #     axis.bar(x=q_num, height=q.data, label=str(m))





class OptParserEmul: