Simulation parameter determination method
First Claim
1. A method of implementing a computer simulation to determine elemental parameters utilizable to reproduce, through computer simulated calculation, experimentally measured values of characteristics or properties of a plurality of analysis objects of any of a plurality of kinds of molecules, materials, parts or structures, where each analysis object is composed of one or more elements and each element of each analysis object has a corresponding elemental type of a plurality of elemental types or has one of a plurality of elemental attribute values, the method comprising:
- (1) storing input data from an input file into a memory unit, the input data specifying;
(1-1) an acceptable error ε
value that corresponds to a maximum acceptable value for a difference between calculated values obtained through simulated calculation and experimental values;
(1-2) a convergence threshold τ
that corresponds to a standard value for judging convergence of calculated values;
(1-3) information necessary for calculating a respective value of each analysis object, and experimental values for each analysis object; and
(1-4) each corresponding elemental type for each element of each analysis object, and each elemental attribute value of each element of each analysis object,(2) executing pre-processing operations using the input data stored in the memory unit comprising;
(2-1) initializing a respective elemental parameter value for each element of each analysis object having a corresponding elemental type according to a respective initialization value for the corresponding elemental type and setting a respective elemental parameter value for each element that does not have a corresponding elemental type as undetermined; and
(2-2) sorting an arrangement order of the analysis objects from lowest to highest number of elements of each analysis object for which the respective elemental parameter value is undetermined utilizing a respective data set for each of the analysis objects that specifies the respective elemental parameter value of each element for the analysis object;
(3) generating a calculation order list by;
(3-1) selecting each analysis object from the plurality of analysis objects that has no more than one element for which the respective elemental parameter value is undetermined, and(3-2) selecting a first analysis object from the plurality of analysis objects that has no more than one element for which the respective elemental parameter value is undetermined, and(3-3) generating the calculation order list according to the arrangement order of analysis objects;
(4) solving a one-variable equation for the respective value of each analysis object by;
(4-1) where the analysis object at a top of the calculation order list has at least one element for which the respective elemental parameter value is undetermined, iteratively solving the one-variable equation for determination of the undetermined respective elemental parameter values for the elements of the analysis object at the top of the calculation order list until an amount of change between iterations of the respective value for the analysis object according to the respective elemental parameter values is less than the convergence threshold;
(4-2) calculating a calculation error as a difference between the value calculated for said analysis object at the top of the calculation order list using the respective elemental parameter values for the elements of the analysis object and a respective experimental value for the analysis object;
(4-3) comparing an absolute value of said calculation error to said acceptable error;
(4-4) where said calculation error for said analysis object at the top of the calculation order list is greater than the acceptable error, resetting the respective elemental parameter values for one of the elements of the analysis object as an undetermined elemental parameter value and returning to step (4-1); and
(4-5) where said calculation error for said analysis object at the top of the calculation order list is equal to or less than the acceptable error, deleting the analysis object from the calculation order; and
then, where an analysis object is present on the top of the calculation order list, returning to step (4-1);
(5) updating elemental parameter values by;
(5-1) updating the respective initialization value for each elemental type as a function of the elemental attribute values of the elements having an elemental attribute value and the elemental parameter values determined by solving the one-variable equation for the respective value of each analysis object;
(5-2) determining at least some of the respective elemental parameter values for each element having a corresponding elemental type as a function of the updated respective initialization value for the corresponding elemental type;
(5-3) sorting the arrangement order of the analysis objects from lowest to highest number of elements of each analysis object for which the respective elemental parameter value is undetermined utilizing the respective data set for each of the analysis objects;
(5-4) sorting between the analysis objects in the arrangement order having the same number of elements for which the respective elemental parameter value is undetermined from lowest to highest number of elements of each analysis object utilizing the respective data set for each of the analysis objects;
(5-5) determining whether any of the respective data sets includes one or more undetermined elemental parameter values, and(6) returning to step (3) if any of the respective data sets includes one or more undetermined elemental parameter values, or outputting the respective data sets of the analysis objects for rendering on an output device and terminating if none of the respective data sets includes one or more undetermined elemental parameter values.
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Abstract
Provided is a method for reducing the amount of calculation time required for parameter determination, and for reducing the amount of calculation time required for parameter determination in satisfaction with a desired accuracy. The method includes preferentially selecting analysis objects, which are capable of providing parameter determination within a high degree of certainty, and controlling a calculation order of the selected analysis objects using a calculation order list.
8 Citations
10 Claims
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1. A method of implementing a computer simulation to determine elemental parameters utilizable to reproduce, through computer simulated calculation, experimentally measured values of characteristics or properties of a plurality of analysis objects of any of a plurality of kinds of molecules, materials, parts or structures, where each analysis object is composed of one or more elements and each element of each analysis object has a corresponding elemental type of a plurality of elemental types or has one of a plurality of elemental attribute values, the method comprising:
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(1) storing input data from an input file into a memory unit, the input data specifying; (1-1) an acceptable error ε
value that corresponds to a maximum acceptable value for a difference between calculated values obtained through simulated calculation and experimental values;(1-2) a convergence threshold τ
that corresponds to a standard value for judging convergence of calculated values;(1-3) information necessary for calculating a respective value of each analysis object, and experimental values for each analysis object; and (1-4) each corresponding elemental type for each element of each analysis object, and each elemental attribute value of each element of each analysis object, (2) executing pre-processing operations using the input data stored in the memory unit comprising; (2-1) initializing a respective elemental parameter value for each element of each analysis object having a corresponding elemental type according to a respective initialization value for the corresponding elemental type and setting a respective elemental parameter value for each element that does not have a corresponding elemental type as undetermined; and (2-2) sorting an arrangement order of the analysis objects from lowest to highest number of elements of each analysis object for which the respective elemental parameter value is undetermined utilizing a respective data set for each of the analysis objects that specifies the respective elemental parameter value of each element for the analysis object; (3) generating a calculation order list by; (3-1) selecting each analysis object from the plurality of analysis objects that has no more than one element for which the respective elemental parameter value is undetermined, and (3-2) selecting a first analysis object from the plurality of analysis objects that has no more than one element for which the respective elemental parameter value is undetermined, and (3-3) generating the calculation order list according to the arrangement order of analysis objects; (4) solving a one-variable equation for the respective value of each analysis object by; (4-1) where the analysis object at a top of the calculation order list has at least one element for which the respective elemental parameter value is undetermined, iteratively solving the one-variable equation for determination of the undetermined respective elemental parameter values for the elements of the analysis object at the top of the calculation order list until an amount of change between iterations of the respective value for the analysis object according to the respective elemental parameter values is less than the convergence threshold; (4-2) calculating a calculation error as a difference between the value calculated for said analysis object at the top of the calculation order list using the respective elemental parameter values for the elements of the analysis object and a respective experimental value for the analysis object; (4-3) comparing an absolute value of said calculation error to said acceptable error; (4-4) where said calculation error for said analysis object at the top of the calculation order list is greater than the acceptable error, resetting the respective elemental parameter values for one of the elements of the analysis object as an undetermined elemental parameter value and returning to step (4-1); and (4-5) where said calculation error for said analysis object at the top of the calculation order list is equal to or less than the acceptable error, deleting the analysis object from the calculation order; and
then, where an analysis object is present on the top of the calculation order list, returning to step (4-1);(5) updating elemental parameter values by; (5-1) updating the respective initialization value for each elemental type as a function of the elemental attribute values of the elements having an elemental attribute value and the elemental parameter values determined by solving the one-variable equation for the respective value of each analysis object; (5-2) determining at least some of the respective elemental parameter values for each element having a corresponding elemental type as a function of the updated respective initialization value for the corresponding elemental type; (5-3) sorting the arrangement order of the analysis objects from lowest to highest number of elements of each analysis object for which the respective elemental parameter value is undetermined utilizing the respective data set for each of the analysis objects; (5-4) sorting between the analysis objects in the arrangement order having the same number of elements for which the respective elemental parameter value is undetermined from lowest to highest number of elements of each analysis object utilizing the respective data set for each of the analysis objects; (5-5) determining whether any of the respective data sets includes one or more undetermined elemental parameter values, and (6) returning to step (3) if any of the respective data sets includes one or more undetermined elemental parameter values, or outputting the respective data sets of the analysis objects for rendering on an output device and terminating if none of the respective data sets includes one or more undetermined elemental parameter values.
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2. A method of implementing a computer simulation to determine elemental parameters utilizable to reproduce, through computer simulated calculation, experimentally measured values of characteristics or properties of a plurality of analysis objects of any of a plurality of kinds of molecules, materials, parts or structures, where each analysis object is composed of one or more elements and each element of each analysis object has a corresponding elemental type of a plurality of elemental types or has one of a plurality of elemental attribute values, the method comprising:
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(1) storing input data from an input file into a memory unit, the input data specifying; (1-1) a convergence threshold τ
that corresponds to a standard value for judging convergence of calculated values;(1-2) for each analysis object, an experimental value or three-dimensional coordinate information of each of the elements of the analysis objects necessary for calculating an experimental value for the analysis object; and (1-3) each corresponding elemental type for each element of each analysis object, and each elemental attribute value of each element of each analysis object, (2) executing pre-processing operations using the input data stored in the memory unit comprising; (2-1) initializing a respective elemental parameter value for each element of each analysis object having a corresponding elemental type according to a respective initialization value for the corresponding elemental type and setting a respective elemental parameter value for each element that does not have a corresponding elemental type as undetermined; and (2-2) sorting an arrangement order of the analysis objects from lowest to highest number of elements of each analysis object for which the respective elemental parameter value is undetermined utilizing a respective data set for each of the analysis objects that specifies the respective elemental parameter value of each element for the analysis object; (3) generating a calculation order list by; (3-1) selecting each analysis object from the plurality of analysis objects that has one element for which the respective elemental parameter value is undetermined, and (3-1) selecting a first analysis object from the plurality of analysis objects that has no more than one element for which the respective elemental parameter value is undetermined, and (3-2) generating the calculation order list according to the arrangement order of the analysis objects (4) solving a one-variable equation for the respective value of each analysis object by; (4-1) for the analysis object at a top of the calculation order list, iteratively solving the one-variable equation for determination of the undetermined respective elemental parameter values for the elements of the analysis object at the top of the calculation order list until an amount of change between iterations of the respective value for the analysis object according to the respective elemental parameter values is less than the convergence threshold; and (4-2) deleting the analysis object from the calculation order; and
then, where an analysis object is present on the top of the calculation order list, returning to step (4-1);(5) updating elemental parameter values by; (5-1) updating the respective initialization value for each elemental type as a function of the elemental attribute values of the elements having an elemental attribute value and the elemental parameter values determined by solving the one-variable equation for the respective value of each analysis object; (5-2) sorting the arrangement order of the analysis objects from lowest to highest number of elements of each analysis object for which the respective elemental parameter value is undetermined utilizing the respective data set for each of the analysis objects; (5-3) sorting between the analysis objects in the arrangement order having the same number of elements for which the respective elemental parameter value is undetermined from lowest to highest number of elements of each analysis object utilizing the respective data set for each of the analysis objects (5-4) determining whether any of the respective data sets of the analysis objects includes one or more undetermined elemental parameter values, and (6) returning to step (3) if any of the respective data sets includes one or more undetermined elemental parameter values, or outputting the respective data sets of the analysis objects for rendering on an output device and terminating if none of the respective data sets includes one or more undetermined elemental parameter values.
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3. A method of implementing a computer simulation to determine atomic parameters utilizable to reproduce, through computer simulated calculation, experimentally measured values of each respective solvation energy of a plurality of kinds of molecules, where each molecule is composed of a plurality of atoms and each atom of each molecule has a corresponding atomic type of a plurality of atomic types or has one of a plurality of atomic attribute values, the method comprising:
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(1) storing input data from an input file into a memory unit, the input data specifying; (1-1) an acceptable energy error ε
value that corresponds to a maximum acceptable value for a difference between calculated values of solvation energy obtained through simulated calculation and experimental values of solvation energy;(1-2) an energy convergence threshold τ
that corresponds to a standard value for judging convergence of calculated values of solvation energy;(1-3) for each molecule, an experimental value of solvation energy or three-dimensional coordinate information of each of the atoms of the molecules necessary for calculating an experimental value of solvation energy for the molecule; and (1-4) each corresponding atomic type for each atom of each molecule, and an atomic attribute value of each atom of each molecule, (2) executing pre-processing operations using the input data stored in the memory unit comprising; (2-1) initializing a respective atomic parameter value for each atom of each molecule having a corresponding atomic type according to a respective initialization value for the corresponding atomic type and setting a respective atomic parameter value for each atom that does not have a corresponding atomic type as undetermined; and (2-2) sorting an arrangement order of the molecules from lowest to highest number of atoms of each molecule for which the respective atomic parameter value is undetermined utilizing a respective data set for each of the molecules that specifies the respective atomic parameter value of each atom for the molecule; (3) generating a calculation order list by; (3-1) selecting each molecule from the plurality of molecules that has no more than one atom for which the respective atomic parameter value is undetermined, and (3-2) selecting a first molecule from the plurality of molecules that has no more than one atom for which the respective atomic parameter value is undetermined, and (3-3) generating the calculation order list according to the arrangement order of the molecules, (4) solving a one-variable equation for the respective value of each molecule by; (4-1) where the molecule at a top of the calculation order list has at least one atom for which the respective atomic parameter value is undetermined, iteratively solving the one-variable equation for determination of the undetermined respective atomic parameter values for the atoms of the molecule at the top of the calculation order list until an amount of change between iterations of the respective value of solvation energy for the molecule according to the respective atomic parameter values is less than the energy convergence threshold; (4-2) calculating a calculation error as a difference between the value of solvation energy calculated for said molecule at the top of the calculation order list using the respective atomic parameter values for the atoms of the molecule and a respective experimental value of solvation energy for the molecule; (4-3) comparing an absolute value of said calculation error to said acceptable energy error; (4-4) where said energy calculation error for said molecule at the top of the calculation order list is greater than the acceptable energy error, resetting the respective atomic parameter values for one of the atoms of the m as an undetermined atomic parameter value and returning to step (4-1); and (4-5) where said calculation error for said molecule at the top of the calculation order list is equal to or less than the acceptable energy error, deleting the molecule from the calculation order; and
then, where a molecule is present on the top of the calculation order list, returning to step (4-1);(5) updating atomic parameter values by; (5-1) updating the respective initialization value for each atomic type as a function of the atomic attribute values of the atoms having an atomic attribute value and the atomic parameter values determined by solving the one-variable equation for the respective value of solvation energy of each molecule; (5-2) determining at least some of the respective atomic parameter values for each atom having a corresponding atomic type as a function of the updated respective initialization value for the corresponding atomic type; (5-3) sorting the arrangement order of the molecules from lowest to highest number of atoms of each molecule for which the respective atomic parameter value is undetermined utilizing the respective data set for each of the molecules; (5-4) sorting between the molecules in the arrangement order having the same number of atoms for which the respective atomic parameter value is undetermined from lowest to highest number of atoms of each molecule utilizing the respective data set for each of the molecules (5-5) determining whether any of the respective data sets of the molecules includes one or more undetermined atomic parameter values, and (6) returning to step (3) if any of the respective data sets includes one or more undetermined atomic parameter values, or outputting the respective data sets of the molecules for rendering on an output device and terminating if none of the respective data sets includes one or more undetermined atomic parameter values.
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4. A method of implementing a computer simulation to determine atomic parameters utilizable to reproduce, through computer simulated calculation, experimentally measured values of each respective solvation energy a plurality of kinds of molecules, where each molecule is composed of a plurality of atoms and each atom of each molecule has a corresponding atomic type of a plurality of atomic types or has one of a plurality of atomic attribute values, the method comprising:
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(1) storing input data from an input file into a memory unit, the input data specifying; (1-1) an energy convergence threshold τ
that corresponds to a standard value for judging convergence of calculated values of solvation energy;(1-3) for each molecule, an experimental value of solvation energy or three-dimensional coordinate information of each of the atoms of the molecules necessary for calculating an experimental value of solvation energy for the molecule; and (1-4) each corresponding atomic type for each atom of each molecule, and an atomic attribute value of each atom of each molecule, (2) executing pre-processing operations using the input data stored in the memory unit comprising; (2-1) initializing a respective atomic parameter value for each atom of each molecule having a corresponding atomic type according to a respective initialization value for the corresponding atomic type and setting a respective atomic parameter value for each atom that does not have a corresponding atomic type as undetermined; and (2-2) sorting an arrangement order of the molecules from lowest to highest number of atoms of each molecule for which the respective atomic parameter value is undetermined utilizing a respective data set for each of the molecules that specifies the respective atomic parameter value of each atom for the molecule; (3) generating a calculation order list by; (3-1) selecting each molecule from the plurality of molecules that has one atom for which the respective atomic parameter value is undetermined, and (3-1) selecting a first molecule from the plurality of molecules that has no more than one atom for which the respective atomic parameter value is undetermined, and (3-2) generating the calculation order list according to the arrangement order of the molecules (4) solving a one-variable equation for the respective value of each molecule by; (4-1) iteratively solving the one-variable equation for determination of the undetermined respective atomic parameter values for the atoms of the molecule at the top of the calculation order list until an amount of change between iterations of the respective value of solvation energy for the molecule according to the respective atomic parameter values is less than the energy convergence threshold; and (4-2) deleting the molecule from the calculation order; and
then, where a molecule is present on the top of the calculation order list, returning to step (4-1);(5) updating atomic parameter values by; (5-1) updating the respective initialization value for each atomic type as a function of the atomic attribute values of the atoms having an atomic attribute value and the atomic parameter values determined by solving the one-variable equation for the respective value of solvation energy of each molecule; (5-2) sorting the arrangement order of the molecules from lowest to highest number of atoms of each molecule for which the respective atomic parameter value is undetermined utilizing the respective data set for each of the molecules; (5-3) sorting between the molecules in the arrangement order having the same number of atoms for which the respective atomic parameter value is undetermined from lowest to highest number of atoms of each molecule utilizing the respective data set for each of the molecules (5-4) determining whether any of the respective data sets of the molecules includes one or more undetermined atomic parameter values, and (6) returning to step (3) if any of the respective data sets includes one or more undetermined atomic parameter values, or outputting the respective data sets of the molecules for rendering on an output device and terminating if none of the respective data sets includes one or more undetermined atomic parameter values.
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5. The method according to claim 3, wherein a user interface is provided with a function that, in generating a calculation order list, upon display of the calculation order list and a selection of one molecule in said calculation order list, an atomic distribution map at a plane formed by atomic charge and averaged bond distance, and a molecular structure map that expresses an atomic parameter determination status of said selected molecule, by a three-dimensional structure of the molecular, and spheres drawn on each atom composing the molecule are displayed in an overlapping manner according to the respective atomic type of an atom of the selected molecule having an undetermined atomic parameter value, and wherein the user interface allows a user to change the calculation order list based on the displayed information by the function.
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6. The method according to claim 4, wherein a user interface is provided with a function that, in generating a calculation order list, upon display of the calculation order list and a selection of one molecule in said calculation order list, an atomic distribution map at a plane formed by atomic charge and averaged bond distance, and a molecular structure map that expresses an atomic parameter determination status of said selected molecule, by a three-dimensional structure of the molecular, and spheres drawn on each atom composing the molecule are displayed in an overlapping manner according to the respective atomic type of an atom of the selected molecule having an undetermined atomic parameter value, and wherein the user interface allows a user to change the calculation order list based on the displayed information by the function.
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7. The method according to claim 3, wherein a user interface is provided with a function that, in generating a calculation order list, after generation of the calculation order list or after a user executes a re-arrangement or a deletion of molecules in the calculation order list, a summary of a calculation status of the molecule is displayed and the number of atomic parameter values and the number of undetermined atomic parameter values of each molecule are displayed.
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8. The method according to claim 4, wherein a user interface is provided with a function that, in generating a calculation order list, after generation of the calculation order list or after a user executes a re-arrangement or a deletion of molecules in the calculation order list, a summary of a calculation status of the molecule is displayed and the number of atomic parameter values and the number of undetermined atomic parameter values of each molecule are displayed.
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9. The method according to claim 3, wherein a user interface is provided with a function that, in updating atomic parameters, a number of all atoms of all molecules, a number of atoms having a determined respective atomic parameter values, a number of atoms having a tentatively determined atomic parameter value, and a number of atoms having an undetermined atomic parameter value are displayed by each atomic type, as an atomic parameter determination status of each atomic type, and upon selection of one atomic type, an atomic parameter value of an atom belonging to said atomic type is displayed in a space formed by atomic charge, averaged bond distance and atomic parameter.
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10. The method according to claim 3, wherein a user interface is provided with a function that, in updating atomic parameters, a number of all atoms of all molecules, a number of atoms having a determined respective atomic parameter values, a number of atoms having a tentatively determined atomic parameter value, and a number of atoms having an undetermined atomic parameter value are displayed by each atomic type, as an atomic parameter determination status of each atomic type, and upon selection of one atomic type, an atomic parameter value of an atom belonging to said atomic type is displayed in a space formed by atomic charge, averaged bond distance and atomic parameter.
Specification